From d912b3ebc5f7a4d3878c58bc955052e3a19c2356 Mon Sep 17 00:00:00 2001 From: Ruitong Li Date: Tue, 5 Aug 2025 10:24:51 -0400 Subject: [PATCH 1/7] converted qmd for compositional --- 04_compositional/propeller.qmd | 195 + 04_compositional/renv.lock | 10241 +++++++++++++++++++++++++++++++ 04_compositional/sccomp.qmd | 179 + 3 files changed, 10615 insertions(+) create mode 100644 04_compositional/propeller.qmd create mode 100644 04_compositional/renv.lock create mode 100644 04_compositional/sccomp.qmd diff --git a/04_compositional/propeller.qmd b/04_compositional/propeller.qmd new file mode 100644 index 0000000..3fd02cc --- /dev/null +++ b/04_compositional/propeller.qmd @@ -0,0 +1,195 @@ +--- +title: "Celltype composition with Propeller" +author: "Harvard Chan Bioinformatics Core" +date: "`r Sys.Date()`" +format: + html: + number-sections: false + default-image-extension: svg + lightbox: true + callout-icon: false + format-links: true + toc: true + theme: sandstone + echo: true + eval: true + message: false + warning: false + code-copy: true + code-overflow: wrap + code-fold: true + code-line-numbers: true + embed-resources: true + standalone: true + html-math-method: katex + grid: + sidebar-width: 250px + body-width: 900px + margin-width: 300px + comments: + hypothesis: true +params: + project_file: ../information.R +knitr: + opts_chunk: + audodep: true + cache: false + cache.lazy: false + error: true + echo: false + fig-height: 5L + fig.retina: 2L + fig-width: 11 + message: false + tidy: true + warning: false +--- + +```{r } +#| message: false +#| warning: false +stopifnot(R.version$major >= 4) # requires R4 +if (compareVersion(R.version$minor, "3.1") < 0) warning("We recommend >= R4.3.1") +stopifnot(compareVersion(as.character(BiocManager::version()), "3.18") >= 0) +stopifnot(compareVersion(as.character(packageVersion("Seurat")), "5.0.0") >= 0) +``` + +This code is in this ![](https://img.shields.io/badge/status-draft-grey) revision. + + +```{r setup} +#| cache: false +#| message: false +#| warning: false +#| echo: false +# knitr::opts_chunk$set(echo = TRUE) +# Load libraries +library(knitr) +library(rmarkdown) + +library(Seurat) +library(SummarizedExperiment) +library(SingleCellExperiment) +library(DEGreport) +library(pheatmap) + +library(tidyverse) +library(data.table) +library(DT) +library(patchwork) + +library(ggprism) +library(grafify) + +library(future) +library(speckle) +# Set seed for reproducibility +set.seed(1454944673L) + +ggplot2::theme_set(theme_prism(base_size = 12)) +# https://grafify-vignettes.netlify.app/colour_palettes.html +# NOTE change colors here if you wish +scale_colour_discrete <- function(...) { + scale_colour_manual(..., values = as.vector(grafify:::graf_palettes[["kelly"]])) +} + +if (future::supportsMulticore()) { + future::plan(future::multicore) +} else { + future::plan(future::multisession) +} +``` + +```{r sanitize_datatable} +sanitize_datatable <- function(df, ...) { + # remove dashes which cause wrapping + DT::datatable(df, ..., + rownames = gsub("-", "_", rownames(df)), + colnames = gsub("-", "_", colnames(df)), + options = list(scrollX = TRUE, ...) + ) +} +``` + +## Load object and subset +Read in the full dataset Seurat object and subset to keep only cells from the conditions of interest (cold7 vs TN). + +```{r load-data} +seurat <- readRDS("data.rds") + +subset_seurat <- subset(x = seurat, subset = condition %in% c("Ctrl", "Treat")) + +Idents(object = subset_seurat) <- "celltype" + +DefaultAssay(subset_seurat) <- "RNA" + +# Create metadata df and factor celltype +meta <- subset_seurat@meta.data +meta$celltype <- factor(meta$celltype) +``` + +## Check count numbers of cells + +```{r cellnumbers} +meta$condition_sample <- paste0(meta$condition, "_", meta$sample) +table(meta$condition_sample, meta$celltype) +``` + +## Run propeller + +```{r run-propeller} +# working code; takes into account cell numbers +# NOTE adapt with your variables of interest +propres <- propeller(subset_seurat, + sample = subset_seurat$sample, + clusters = subset_seurat$celltype, + group = subset_seurat$condition +) + +sanitize_datatable(propres) +``` + +## Proportions of cells table + +To understand discordance with sccomp results, let's evaluate proportions and variability within group. + + +```{r} +props <- getTransformedProps(meta$celltype, + meta$condition_sample, + transform = "logit" +) + +props$Proportions +``` + +```{r extracode} +#| eval: false +meta_propeller <- meta %>% + group_by(condition, sample) %>% + distinct(sample) + +designAS <- model.matrix(~ meta_propeller$condition) +colnames(designAS) <- c("Ctrl", "Treat") + +fit <- lmFit(props$TransformedProps, designAS) +fit <- eBayes(fit, robust = TRUE) + +topTable(fit) +``` +# Resources + +* [Speckle vignette](http://127.0.0.1:29356/library/speckle/doc/speckle.html#finding-significant-differences-in-cell-type-proportions-using-propeller) +* [Application to mouse PBMC scRNA](https://phipsonlab.github.io/propeller-paper-analysis/RealDataAnalysis.html#Young_vs_Old) + +# Conclusion + +# R session + +List and version of tools used for the QC report generation. + +```{r} +sessionInfo() +``` + + diff --git a/04_compositional/renv.lock b/04_compositional/renv.lock new file mode 100644 index 0000000..28df0cf --- /dev/null +++ b/04_compositional/renv.lock @@ -0,0 +1,10241 @@ +{ + "R": { + "Version": "4.5.0", + "Repositories": [ + { + "Name": "BioCsoft", + "URL": "https://bioconductor.org/packages/3.21/bioc" + }, + { + "Name": "BioCann", + "URL": "https://bioconductor.org/packages/3.21/data/annotation" + }, + { + "Name": "BioCexp", + "URL": "https://bioconductor.org/packages/3.21/data/experiment" + }, + { + "Name": "BioCworkflows", + "URL": "https://bioconductor.org/packages/3.21/workflows" + }, + { + "Name": "BioCbooks", + "URL": "https://bioconductor.org/packages/3.21/books" + }, + { + "Name": "CRAN", + "URL": "https://packagemanager.posit.co/cran/latest" + } + ] + }, + "Bioconductor": { + "Version": "3.21" + }, + "Packages": { + "ALL": { + "Package": "ALL", + "Version": "1.50.0", + "Source": "Bioconductor", + "Title": "A data package", + "Date": "2009-07-22", + "Author": "Xiaochun Li", + "Description": "Data of T- and B-cell Acute Lymphocytic Leukemia from the Ritz Laboratory at the DFCI (includes Apr 2004 versions)", + "Maintainer": "Robert Gentleman ", + "License": "Artistic-2.0", + "Depends": [ + "R (>= 2.10)", + "Biobase (>= 2.5.5)" + ], + "Suggests": [ + "rpart" + ], + "biocViews": "ExperimentData, CancerData, LeukemiaCancerData", + "git_url": "https://git.bioconductor.org/packages/ALL", + "git_branch": "RELEASE_3_21", + "git_last_commit": "81e0f2f", + "git_last_commit_date": "2025-04-15", + "Repository": "Bioconductor 3.21", + "NeedsCompilation": "no" + }, + "BH": { + "Package": "BH", + "Version": "1.87.0-1", + "Source": "Repository", + "Type": "Package", + "Title": "Boost C++ Header Files", + "Date": "2024-12-17", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"John W.\", \"Emerson\", role = \"aut\"), person(\"Michael J.\", \"Kane\", role = \"aut\", comment = c(ORCID = \"0000-0003-1899-6662\")))", + "Description": "Boost provides free peer-reviewed portable C++ source libraries. 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See file COPYRIGHT for details\") )", + "Description": "Finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3). There is support for approximate as well as exact searches, fixed radius searches and 'bd' as well as 'kd' trees. The distance is computed using the L2 (Euclidean) metric. Please see package 'RANN.L1' for the same functionality using the L1 (Manhattan, taxicab) metric.", + "License": "GPL (>= 3)", + "URL": "https://github.com/jefferislab/RANN, https://jefferislab.github.io/RANN/", + "BugReports": "https://github.com/jefferislab/RANN/issues", + "Suggests": [ + "testthat" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Gregory Jefferis [aut, cre] (), Samuel E. Kemp [aut], Kirill Müller [ctb] (), Sunil Arya [aut, cph] (), David Mount [aut, cph] (), University of Maryland [cph] (ANN library is copyright University of Maryland and Sunil Arya and David Mount. See file COPYRIGHT for details)", + "Maintainer": "Gregory Jefferis ", + "Repository": "CRAN" + }, + "RColorBrewer": { + "Package": "RColorBrewer", + "Version": "1.1-3", + "Source": "Repository", + "Date": "2022-04-03", + "Title": "ColorBrewer Palettes", + "Authors@R": "c(person(given = \"Erich\", family = \"Neuwirth\", role = c(\"aut\", \"cre\"), email = \"erich.neuwirth@univie.ac.at\"))", + "Author": "Erich Neuwirth [aut, cre]", + "Maintainer": "Erich Neuwirth ", + "Depends": [ + "R (>= 2.0.0)" + ], + "Description": "Provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org.", + "License": "Apache License 2.0", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, + "ROCR": { + "Package": "ROCR", + "Version": "1.0-11", + "Source": "Repository", + "Authors@R": "c(person(\"Tobias\",\"Sing\", email = \"tobias.sing@gmail.com\",role=\"aut\"), person(\"Oliver\",\"Sander\", email = \"osander@gmail.com\",role=\"aut\"), person(\"Niko\",\"Beerenwinkel\", role=\"aut\"), person(\"Thomas\",\"Lengauer\", role=\"aut\"), person(\"Thomas\",\"Unterthiner\", role=\"ctb\"), person(\"Felix G.M.\",\"Ernst\", email = \"felix.gm.ernst@outlook.com\",role=\"cre\", comment = c(ORCID = \"0000-0001-5064-0928\")))", + "Date": "2020-05-01", + "Title": "Visualizing the Performance of Scoring Classifiers", + "Description": "ROC graphs, sensitivity/specificity curves, lift charts, and precision/recall plots are popular examples of trade-off visualizations for specific pairs of performance measures. ROCR is a flexible tool for creating cutoff-parameterized 2D performance curves by freely combining two from over 25 performance measures (new performance measures can be added using a standard interface). Curves from different cross-validation or bootstrapping runs can be averaged by different methods, and standard deviations, standard errors or box plots can be used to visualize the variability across the runs. The parameterization can be visualized by printing cutoff values at the corresponding curve positions, or by coloring the curve according to cutoff. All components of a performance plot can be quickly adjusted using a flexible parameter dispatching mechanism. Despite its flexibility, ROCR is easy to use, with only three commands and reasonable default values for all optional parameters.", + "Encoding": "UTF-8", + "License": "GPL (>= 2)", + "NeedsCompilation": "no", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "methods", + "graphics", + "grDevices", + "gplots", + "stats" + ], + "Suggests": [ + "testthat", + "knitr", + "rmarkdown" + ], + "URL": "http://ipa-tys.github.io/ROCR/", + "BugReports": "https://github.com/ipa-tys/ROCR/issues", + "RoxygenNote": "7.1.0", + "VignetteBuilder": "knitr", + "Author": "Tobias Sing [aut], Oliver Sander [aut], Niko Beerenwinkel [aut], Thomas Lengauer [aut], Thomas Unterthiner [ctb], Felix G.M. Ernst [cre] ()", + "Maintainer": "Felix G.M. Ernst ", + "Repository": "CRAN" + }, + "RSpectra": { + "Package": "RSpectra", + "Version": "0.16-2", + "Source": "Repository", + "Type": "Package", + "Title": "Solvers for Large-Scale Eigenvalue and SVD Problems", + "Date": "2024-07-18", + "Authors@R": "c( person(\"Yixuan\", \"Qiu\", , \"yixuan.qiu@cos.name\", c(\"aut\", \"cre\")), person(\"Jiali\", \"Mei\", , \"vermouthmjl@gmail.com\", \"aut\", comment = \"Function interface of matrix operation\"), person(\"Gael\", \"Guennebaud\", , \"gael.guennebaud@inria.fr\", \"ctb\", comment = \"Eigenvalue solvers from the 'Eigen' library\"), person(\"Jitse\", \"Niesen\", , \"jitse@maths.leeds.ac.uk\", \"ctb\", comment = \"Eigenvalue solvers from the 'Eigen' library\") )", + "Description": "R interface to the 'Spectra' library for large-scale eigenvalue and SVD problems. It is typically used to compute a few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues, which is usually more efficient than eigen() if k << n. This package provides the 'eigs()' function that does the similar job as in 'Matlab', 'Octave', 'Python SciPy' and 'Julia'. It also provides the 'svds()' function to calculate the largest k singular values and corresponding singular vectors of a real matrix. The matrix to be computed on can be dense, sparse, or in the form of an operator defined by the user.", + "License": "MPL (>= 2)", + "URL": "https://github.com/yixuan/RSpectra", + "BugReports": "https://github.com/yixuan/RSpectra/issues", + "Depends": [ + "R (>= 3.0.2)" + ], + "Imports": [ + "Matrix (>= 1.1-0)", + "Rcpp (>= 0.11.5)" + ], + "Suggests": [ + "knitr", + "rmarkdown", + "prettydoc" + ], + "LinkingTo": [ + "Rcpp", + "RcppEigen (>= 0.3.3.3.0)" + ], + "VignetteBuilder": "knitr, rmarkdown", + "RoxygenNote": "7.1.2", + "NeedsCompilation": "yes", + "Author": "Yixuan Qiu [aut, cre], Jiali Mei [aut] (Function interface of matrix operation), Gael Guennebaud [ctb] (Eigenvalue solvers from the 'Eigen' library), Jitse Niesen [ctb] (Eigenvalue solvers from the 'Eigen' library)", + "Maintainer": "Yixuan Qiu ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "Rcpp": { + "Package": "Rcpp", + "Version": "1.0.14", + "Source": "Repository", + "Title": "Seamless R and C++ Integration", + "Date": "2025-01-11", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"JJ\", \"Allaire\", role = \"aut\", comment = c(ORCID = \"0000-0003-0174-9868\")), person(\"Kevin\", \"Ushey\", role = \"aut\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Qiang\", \"Kou\", role = \"aut\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Nathan\", \"Russell\", role = \"aut\"), person(\"Iñaki\", \"Ucar\", role = \"aut\", comment = c(ORCID = \"0000-0001-6403-5550\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"John\", \"Chambers\", role = \"aut\"))", + "Description": "The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at , the paper by Eddelbuettel and Francois (2011, ), the book by Eddelbuettel (2013, ) and the paper by Eddelbuettel and Balamuta (2018, ); see 'citation(\"Rcpp\")' for details.", + "Imports": [ + "methods", + "utils" + ], + "Suggests": [ + "tinytest", + "inline", + "rbenchmark", + "pkgKitten (>= 0.1.2)" + ], + "URL": "https://www.rcpp.org, https://dirk.eddelbuettel.com/code/rcpp.html, https://github.com/RcppCore/Rcpp", + "License": "GPL (>= 2)", + "BugReports": "https://github.com/RcppCore/Rcpp/issues", + "MailingList": "rcpp-devel@lists.r-forge.r-project.org", + "RoxygenNote": "6.1.1", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (), Romain Francois [aut] (), JJ Allaire [aut] (), Kevin Ushey [aut] (), Qiang Kou [aut] (), Nathan Russell [aut], Iñaki Ucar [aut] (), Doug Bates [aut] (), John Chambers [aut]", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" + }, + "RcppAnnoy": { + "Package": "RcppAnnoy", + "Version": "0.0.22", + "Source": "Repository", + "Type": "Package", + "Title": "'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest Neighbors", + "Date": "2024-01-23", + "Author": "Dirk Eddelbuettel", + "Maintainer": "Dirk Eddelbuettel ", + "Description": "'Annoy' is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from / save to disk. This package provides an R interface by relying on the 'Rcpp' package, exposing the same interface as the original Python wrapper to 'Annoy'. See for more on 'Annoy'. 'Annoy' is released under Version 2.0 of the Apache License. Also included is a small Windows port of 'mmap' which is released under the MIT license.", + "License": "GPL (>= 2)", + "Depends": [ + "R (>= 3.1)" + ], + "Imports": [ + "methods", + "Rcpp" + ], + "LinkingTo": [ + "Rcpp" + ], + "Suggests": [ + "tinytest" + ], + "URL": "https://github.com/eddelbuettel/rcppannoy, https://dirk.eddelbuettel.com/code/rcpp.annoy.html", + "BugReports": "https://github.com/eddelbuettel/rcppannoy/issues", + "NeedsCompilation": "yes", + "RoxygenNote": "7.1.1", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "RcppArmadillo": { + "Package": "RcppArmadillo", + "Version": "14.6.0-1", + "Source": "Repository", + "Type": "Package", + "Title": "'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library", + "Date": "2025-07-02", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Binxiang\", \"Ni\", role = \"aut\"), person(\"Conrad\", \"Sanderson\", role = \"aut\", comment = c(ORCID = \"0000-0002-0049-4501\")))", + "Description": "'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed under Apache License 2; previous releases were under licensed as MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that; 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.", + "License": "GPL (>= 2)", + "LazyLoad": "yes", + "Depends": [ + "R (>= 3.3.0)" + ], + "LinkingTo": [ + "Rcpp" + ], + "Imports": [ + "Rcpp (>= 1.0.12)", + "stats", + "utils", + "methods" + ], + "Suggests": [ + "tinytest", + "Matrix (>= 1.3.0)", + "pkgKitten", + "reticulate", + "slam" + ], + "URL": "https://github.com/RcppCore/RcppArmadillo, https://dirk.eddelbuettel.com/code/rcpp.armadillo.html", + "BugReports": "https://github.com/RcppCore/RcppArmadillo/issues", + "RoxygenNote": "6.0.1", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Romain Francois [aut] (ORCID: ), Doug Bates [aut] (ORCID: ), Binxiang Ni [aut], Conrad Sanderson [aut] (ORCID: )", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "RcppEigen": { + "Package": "RcppEigen", + "Version": "0.3.4.0.2", + "Source": "Repository", + "Type": "Package", + "Title": "'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library", + "Date": "2024-08-23", + "Authors@R": "c(person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Yixuan\", \"Qiu\", role = \"aut\", comment = c(ORCID = \"0000-0003-0109-6692\")), person(\"Authors of\", \"Eigen\", role = \"cph\", comment = \"Authorship and copyright in included Eigen library as detailed in inst/COPYRIGHTS\"))", + "Copyright": "See the file COPYRIGHTS for various Eigen copyright details", + "Description": "R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems. Its performance on many algorithms is comparable with some of the best implementations based on 'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header files from the 'Eigen' C++ template library. Thus users do not need to install 'Eigen' itself in order to use 'RcppEigen'. Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2); earlier version were licensed under the GNU LGPL version 3 or later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.", + "License": "GPL (>= 2) | file LICENSE", + "LazyLoad": "yes", + "Depends": [ + "R (>= 3.6.0)" + ], + "LinkingTo": [ + "Rcpp" + ], + "Imports": [ + "Rcpp (>= 0.11.0)", + "stats", + "utils" + ], + "Suggests": [ + "Matrix", + "inline", + "tinytest", + "pkgKitten", + "microbenchmark" + ], + "URL": "https://github.com/RcppCore/RcppEigen, https://dirk.eddelbuettel.com/code/rcpp.eigen.html", + "BugReports": "https://github.com/RcppCore/RcppEigen/issues", + "NeedsCompilation": "yes", + "Author": "Doug Bates [aut] (), Dirk Eddelbuettel [aut, cre] (), Romain Francois [aut] (), Yixuan Qiu [aut] (), Authors of Eigen [cph] (Authorship and copyright in included Eigen library as detailed in inst/COPYRIGHTS)", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" + }, + "RcppHNSW": { + "Package": "RcppHNSW", + "Version": "0.6.0", + "Source": "Repository", + "Title": "'Rcpp' Bindings for 'hnswlib', a Library for Approximate Nearest Neighbors", + "Authors@R": "c( person(\"James\", \"Melville\", , \"jlmelville@gmail.com\", role = c(\"aut\", \"cre\", \"cph\")), person(\"Aaron\", \"Lun\", role = \"ctb\"), person(\"Samuel\", \"Granjeaud\", role = \"ctb\"), person(\"Dmitriy\", \"Selivanov\", role = \"ctb\"), person(\"Yuxing\", \"Liao\", role = \"ctb\") )", + "Description": "'Hnswlib' is a C++ library for Approximate Nearest Neighbors. This package provides a minimal R interface by relying on the 'Rcpp' package. See for more on 'hnswlib'. 'hnswlib' is released under Version 2.0 of the Apache License.", + "License": "GPL (>= 3)", + "URL": "https://github.com/jlmelville/rcpphnsw", + "BugReports": "https://github.com/jlmelville/rcpphnsw/issues", + "Imports": [ + "methods", + "Rcpp (>= 0.11.3)" + ], + "Suggests": [ + "covr", + "testthat" + ], + "LinkingTo": [ + "Rcpp" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "James Melville [aut, cre, cph], Aaron Lun [ctb], Samuel Granjeaud [ctb], Dmitriy Selivanov [ctb], Yuxing Liao [ctb]", + "Maintainer": "James Melville ", + "Repository": "CRAN" + }, + "RcppProgress": { + "Package": "RcppProgress", + "Version": "0.4.2", + "Source": "Repository", + "Maintainer": "Karl Forner ", + "License": "GPL (>= 3)", + "Title": "An Interruptible Progress Bar with OpenMP Support for C++ in R Packages", + "Type": "Package", + "LazyLoad": "yes", + "Author": "Karl Forner ", + "Description": "Allows to display a progress bar in the R console for long running computations taking place in c++ code, and support for interrupting those computations even in multithreaded code, typically using OpenMP.", + "URL": "https://github.com/kforner/rcpp_progress", + "BugReports": "https://github.com/kforner/rcpp_progress/issues", + "Date": "2020-02-06", + "Suggests": [ + "RcppArmadillo", + "devtools", + "roxygen2", + "testthat" + ], + "RoxygenNote": "6.1.1", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, + "RcppTOML": { + "Package": "RcppTOML", + "Version": "0.2.3", + "Source": "Repository", + "Type": "Package", + "Title": "'Rcpp' Bindings to Parser for \"Tom's Obvious Markup Language\"", + "Date": "2025-03-08", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Mark\", \"Gillard\", role = \"aut\", comment = \"Author of 'toml++' header library\"))", + "Description": "The configuration format defined by 'TOML' (which expands to \"Tom's Obvious Markup Language\") specifies an excellent format (described at ) suitable for both human editing as well as the common uses of a machine-readable format. This package uses 'Rcpp' to connect to the 'toml++' parser written by Mark Gillard to R.", + "SystemRequirements": "A C++17 compiler", + "BugReports": "https://github.com/eddelbuettel/rcpptoml/issues", + "URL": "http://dirk.eddelbuettel.com/code/rcpp.toml.html", + "Imports": [ + "Rcpp (>= 1.0.8)" + ], + "Depends": [ + "R (>= 3.3.0)" + ], + "LinkingTo": [ + "Rcpp" + ], + "Suggests": [ + "tinytest" + ], + "License": "GPL (>= 2)", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (), Mark Gillard [aut] (Author of 'toml++' header library)", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" + }, + "Rdpack": { + "Package": "Rdpack", + "Version": "2.6.4", + "Source": "Repository", + "Type": "Package", + "Title": "Update and Manipulate Rd Documentation Objects", + "Authors@R": "c( person(given = c(\"Georgi\", \"N.\"), family = \"Boshnakov\", role = c(\"aut\", \"cre\"), email = \"georgi.boshnakov@manchester.ac.uk\", comment = c(ORCID = \"0000-0003-2839-346X\")), person(given = \"Duncan\", family = \"Murdoch\", role = \"ctb\", email = \"murdoch.duncan@gmail.com\") )", + "Description": "Functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating 'Rd' documentation for functions, methods and classes; 'Rd' macros for citations and import of references from 'bibtex' files for use in 'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and inserting snippets of 'R' code and the results of its evaluation or creating graphics on the fly; and many functions for manipulation of references and Rd files.", + "URL": "https://geobosh.github.io/Rdpack/ (doc), https://github.com/GeoBosh/Rdpack (devel)", + "BugReports": "https://github.com/GeoBosh/Rdpack/issues", + "Depends": [ + "R (>= 2.15.0)", + "methods" + ], + "Imports": [ + "tools", + "utils", + "rbibutils (>= 1.3)" + ], + "Suggests": [ + "grDevices", + "testthat", + "rstudioapi", + "rprojroot", + "gbRd" + ], + "License": "GPL (>= 2)", + "LazyLoad": "yes", + "RoxygenNote": "7.1.1", + "NeedsCompilation": "no", + "Author": "Georgi N. 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\"0000-0001-9373-2726\")), person(given = \"R. Willem\", family = \"Vervoort\", role = \"ctb\", email = \"Willemvervoort@gmail.com\"), person(given = \"Brenton M.\", family = \"Wiernik\", role = \"ctb\", email = \"brenton@wiernik.org\"), person(given = \"Josh\", family = \"Yamamoto\", role = \"ctb\", email = \"joshuayamamoto5@gmail.com\"), person(given = \"Jasme\", family = \"Lee\", role = \"ctb\"), person(given = \"Taren\", family = \"Sanders\", role = \"ctb\", email = \"taren.sanders@acu.edu.au\", comment = c(ORCID = \"0000-0002-4504-6008\")), person(given = \"Ilaria\", family = \"Prosdocimi\", role = \"ctb\", email = \"prosdocimi.ilaria@gmail.com\", comment = c(ORCID = \"0000-0001-8565-094X\")), person(given = \"Daniel D.\", family = \"Sjoberg\", role = \"ctb\", email = \"danield.sjoberg@gmail.com\", comment = c(ORCID = \"0000-0003-0862-2018\")), person(given = \"Alex\", family = \"Reinhart\", role = \"ctb\", email = \"areinhar@stat.cmu.edu\", comment = c(ORCID = \"0000-0002-6658-514X\")))", + "Description": "Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.", + "License": "MIT + file LICENSE", + "URL": "https://broom.tidymodels.org/, https://github.com/tidymodels/broom", + "BugReports": "https://github.com/tidymodels/broom/issues", + "Depends": [ + "R (>= 3.5)" + ], + "Imports": [ + "backports", + "cli", + "dplyr (>= 1.0.0)", + "generics (>= 0.0.2)", + "glue", + "lifecycle", + "purrr", + "rlang (>= 1.1.0)", + "stringr", + "tibble (>= 3.0.0)", + "tidyr (>= 1.0.0)" + ], + "Suggests": [ + "AER", + "AUC", + "bbmle", + "betareg (>= 3.2-1)", + "biglm", + "binGroup", + "boot", + "btergm (>= 1.10.6)", + "car (>= 3.1-2)", + "carData", + "caret", + "cluster", + "cmprsk", + "coda", + "covr", + "drc", + "e1071", + "emmeans", + "epiR", + "ergm (>= 3.10.4)", + "fixest (>= 0.9.0)", + "gam (>= 1.15)", + "gee", + "geepack", + "ggplot2", + "glmnet", + "glmnetUtils", + "gmm", + "Hmisc", + "irlba", + "interp", + "joineRML", + "Kendall", + "knitr", + "ks", + "Lahman", + "lavaan (>= 0.6.18)", + "leaps", + "lfe", + "lm.beta", + "lme4", + "lmodel2", + "lmtest (>= 0.9.38)", + "lsmeans", + "maps", + "margins", + "MASS", + "mclust", + "mediation", + "metafor", + "mfx", + "mgcv", + "mlogit", + "modeldata", + "modeltests (>= 0.1.6)", + "muhaz", + "multcomp", + "network", + "nnet", + "ordinal", + "plm", + "poLCA", + "psych", + "quantreg", + "rmarkdown", + "robust", + "robustbase", + "rsample", + "sandwich", + "spdep (>= 1.1)", + "spatialreg", + "speedglm", + "spelling", + "survey", + "survival (>= 3.6-4)", + "systemfit", + "testthat (>= 3.0.0)", + "tseries", + "vars", + "zoo" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Language": "en-US", + "Collate": "'aaa-documentation-helper.R' 'null-and-default.R' 'aer.R' 'auc.R' 'base.R' 'bbmle.R' 'betareg.R' 'biglm.R' 'bingroup.R' 'boot.R' 'broom-package.R' 'broom.R' 'btergm.R' 'car.R' 'caret.R' 'cluster.R' 'cmprsk.R' 'data-frame.R' 'deprecated-0-7-0.R' 'drc.R' 'emmeans.R' 'epiR.R' 'ergm.R' 'fixest.R' 'gam.R' 'geepack.R' 'glmnet-cv-glmnet.R' 'glmnet-glmnet.R' 'gmm.R' 'hmisc.R' 'import-standalone-obj-type.R' 'import-standalone-types-check.R' 'joinerml.R' 'kendall.R' 'ks.R' 'lavaan.R' 'leaps.R' 'lfe.R' 'list-irlba.R' 'list-optim.R' 'list-svd.R' 'list-xyz.R' 'list.R' 'lm-beta.R' 'lmodel2.R' 'lmtest.R' 'maps.R' 'margins.R' 'mass-fitdistr.R' 'mass-negbin.R' 'mass-polr.R' 'mass-ridgelm.R' 'stats-lm.R' 'mass-rlm.R' 'mclust.R' 'mediation.R' 'metafor.R' 'mfx.R' 'mgcv.R' 'mlogit.R' 'muhaz.R' 'multcomp.R' 'nnet.R' 'nobs.R' 'ordinal-clm.R' 'ordinal-clmm.R' 'plm.R' 'polca.R' 'psych.R' 'stats-nls.R' 'quantreg-nlrq.R' 'quantreg-rq.R' 'quantreg-rqs.R' 'robust-glmrob.R' 'robust-lmrob.R' 'robustbase-glmrob.R' 'robustbase-lmrob.R' 'sp.R' 'spdep.R' 'speedglm-speedglm.R' 'speedglm-speedlm.R' 'stats-anova.R' 'stats-arima.R' 'stats-decompose.R' 'stats-factanal.R' 'stats-glm.R' 'stats-htest.R' 'stats-kmeans.R' 'stats-loess.R' 'stats-mlm.R' 'stats-prcomp.R' 'stats-smooth.spline.R' 'stats-summary-lm.R' 'stats-time-series.R' 'survey.R' 'survival-aareg.R' 'survival-cch.R' 'survival-coxph.R' 'survival-pyears.R' 'survival-survdiff.R' 'survival-survexp.R' 'survival-survfit.R' 'survival-survreg.R' 'systemfit.R' 'tseries.R' 'utilities.R' 'vars.R' 'zoo.R' 'zzz.R'", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "David Robinson [aut], Alex Hayes [aut] (), Simon Couch [aut, cre] (), Posit Software, PBC [cph, fnd], Indrajeet Patil [ctb] (), Derek Chiu [ctb], Matthieu Gomez [ctb], Boris Demeshev [ctb], Dieter Menne [ctb], Benjamin Nutter [ctb], Luke Johnston [ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb], Matthew Lincoln [ctb], Alessandro Gasparini [ctb], Lukasz Komsta [ctb], Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Karissa Whiting [ctb], Yves Rosseel [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb] (), Ethan Christensen [ctb], Steven Pav [ctb], Paul PJ [ctb], Ben Schneider [ctb], Patrick Kennedy [ctb], Lily Medina [ctb], Brian Fannin [ctb], Jason Muhlenkamp [ctb], Matt Lehman [ctb], Bill Denney [ctb] (), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (), Jasper Cooper [ctb] (), E Auden Krauska [ctb] (), Alex Wang [ctb], Malcolm Barrett [ctb] (), Charles Gray [ctb] (), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (), Eduard Szoecs [ctb], Frederik Aust [ctb] (), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (), Bruna Wundervald [ctb] (), Joyce Cahoon [ctb] (), Grant McDermott [ctb] (), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (), Lukas Wallrich [ctb] (), James Martherus [ctb] (), Chuliang Xiao [ctb] (), Joseph Larmarange [ctb], Max Kuhn [ctb], Michal Bojanowski [ctb], Hakon Malmedal [ctb], Clara Wang [ctb], Sergio Oller [ctb], Luke Sonnet [ctb], Jim Hester [ctb], Ben Schneider [ctb], Bernie Gray [ctb] (), Mara Averick [ctb], Aaron Jacobs [ctb], Andreas Bender [ctb], Sven Templer [ctb], Paul-Christian Buerkner [ctb], Matthew Kay [ctb], Erwan Le Pennec [ctb], Johan Junkka [ctb], Hao Zhu [ctb], Benjamin Soltoff [ctb], Zoe Wilkinson Saldana [ctb], Tyler Littlefield [ctb], Charles T. Gray [ctb], Shabbh E. Banks [ctb], Serina Robinson [ctb], Roger Bivand [ctb], Riinu Ots [ctb], Nicholas Williams [ctb], Nina Jakobsen [ctb], Michael Weylandt [ctb], Lisa Lendway [ctb], Karl Hailperin [ctb], Josue Rodriguez [ctb], Jenny Bryan [ctb], Chris Jarvis [ctb], Greg Macfarlane [ctb], Brian Mannakee [ctb], Drew Tyre [ctb], Shreyas Singh [ctb], Laurens Geffert [ctb], Hong Ooi [ctb], Henrik Bengtsson [ctb], Eduard Szocs [ctb], David Hugh-Jones [ctb], Matthieu Stigler [ctb], Hugo Tavares [ctb] (), R. Willem Vervoort [ctb], Brenton M. Wiernik [ctb], Josh Yamamoto [ctb], Jasme Lee [ctb], Taren Sanders [ctb] (), Ilaria Prosdocimi [ctb] (), Daniel D. Sjoberg [ctb] (), Alex Reinhart [ctb] ()", + "Maintainer": "Simon Couch ", + "Repository": "CRAN" + }, + "bslib": { + "Package": "bslib", + "Version": "0.9.0", + "Source": "Repository", + "Title": "Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'", + "Authors@R": "c( person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Garrick\", \"Aden-Buie\", , \"garrick@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-7111-0077\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(, \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Javi\", \"Aguilar\", role = c(\"ctb\", \"cph\"), comment = \"Bootstrap colorpicker library\"), person(\"Thomas\", \"Park\", role = c(\"ctb\", \"cph\"), comment = \"Bootswatch library\"), person(, \"PayPal\", role = c(\"ctb\", \"cph\"), comment = \"Bootstrap accessibility plugin\") )", + "Description": "Simplifies custom 'CSS' styling of both 'shiny' and 'rmarkdown' via 'Bootstrap' 'Sass'. Supports 'Bootstrap' 3, 4 and 5 as well as their various 'Bootswatch' themes. 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Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".", + "Maintainer": "Martin Maechler ", + "Authors@R": "c(person(\"Martin\",\"Maechler\", role = c(\"aut\",\"cre\"), email=\"maechler@stat.math.ethz.ch\", comment = c(ORCID = \"0000-0002-8685-9910\")) ,person(\"Peter\", \"Rousseeuw\", role=\"aut\", email=\"peter.rousseeuw@kuleuven.be\", comment = c(\"Fortran original\", ORCID = \"0000-0002-3807-5353\")) ,person(\"Anja\", \"Struyf\", role=\"aut\", comment= \"S original\") ,person(\"Mia\", \"Hubert\", role=\"aut\", email= \"Mia.Hubert@uia.ua.ac.be\", comment = c(\"S original\", ORCID = \"0000-0001-6398-4850\")) ,person(\"Kurt\", \"Hornik\", role=c(\"trl\", \"ctb\"), email=\"Kurt.Hornik@R-project.org\", comment=c(\"port to R; maintenance(1999-2000)\", ORCID=\"0000-0003-4198-9911\")) ,person(\"Matthias\", \"Studer\", role=\"ctb\") ,person(\"Pierre\", \"Roudier\", role=\"ctb\") ,person(\"Juan\", \"Gonzalez\", role=\"ctb\") ,person(\"Kamil\", \"Kozlowski\", role=\"ctb\") ,person(\"Erich\", \"Schubert\", role=\"ctb\", comment = c(\"fastpam options for pam()\", ORCID = \"0000-0001-9143-4880\")) ,person(\"Keefe\", \"Murphy\", role=\"ctb\", comment = \"volume.ellipsoid({d >= 3})\") #not yet ,person(\"Fischer-Rasmussen\", \"Kasper\", role = \"ctb\", comment = \"Gower distance for CLARA\") )", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "graphics", + "grDevices", + "stats", + "utils" + ], + "Suggests": [ + "MASS", + "Matrix" + ], + "SuggestsNote": "MASS: two examples using cov.rob() and mvrnorm(); Matrix tools for testing", + "Enhances": [ + "mvoutlier", + "fpc", + "ellipse", + "sfsmisc" + ], + "EnhancesNote": "xref-ed in man/*.Rd", + "LazyLoad": "yes", + "LazyData": "yes", + "ByteCompile": "yes", + "BuildResaveData": "no", + "License": "GPL (>= 2)", + "URL": "https://svn.r-project.org/R-packages/trunk/cluster/", + "NeedsCompilation": "yes", + "Author": "Martin Maechler [aut, cre] (), Peter Rousseeuw [aut] (Fortran original, ), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original, ), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000), ), Matthias Studer [ctb], Pierre Roudier [ctb], Juan Gonzalez [ctb], Kamil Kozlowski [ctb], Erich Schubert [ctb] (fastpam options for pam(), ), Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))", + "Repository": "CRAN" + }, + "codetools": { + "Package": "codetools", + "Version": "0.2-20", + "Source": "Repository", + "Priority": "recommended", + "Author": "Luke Tierney ", + "Description": "Code analysis tools for R.", + "Title": "Code Analysis Tools for R", + "Depends": [ + "R (>= 2.1)" + ], + "Maintainer": "Luke Tierney ", + "URL": "https://gitlab.com/luke-tierney/codetools", + "License": "GPL", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, + "colorspace": { + "Package": "colorspace", + "Version": "2.1-1", + "Source": "Repository", + "Date": "2024-07-26", + "Title": "A Toolbox for Manipulating and Assessing Colors and Palettes", + "Authors@R": "c(person(given = \"Ross\", family = \"Ihaka\", role = \"aut\", email = \"ihaka@stat.auckland.ac.nz\"), person(given = \"Paul\", family = \"Murrell\", role = \"aut\", email = \"paul@stat.auckland.ac.nz\", comment = c(ORCID = \"0000-0002-3224-8858\")), person(given = \"Kurt\", family = \"Hornik\", role = \"aut\", email = \"Kurt.Hornik@R-project.org\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(given = c(\"Jason\", \"C.\"), family = \"Fisher\", role = \"aut\", email = \"jfisher@usgs.gov\", comment = c(ORCID = \"0000-0001-9032-8912\")), person(given = \"Reto\", family = \"Stauffer\", role = \"aut\", email = \"Reto.Stauffer@uibk.ac.at\", comment = c(ORCID = \"0000-0002-3798-5507\")), person(given = c(\"Claus\", \"O.\"), family = \"Wilke\", role = \"aut\", email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(given = c(\"Claire\", \"D.\"), family = \"McWhite\", role = \"aut\", email = \"claire.mcwhite@utmail.utexas.edu\", comment = c(ORCID = \"0000-0001-7346-3047\")), person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")))", + "Description": "Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided along with corresponding ggplot2 color scales. Color palette choice is aided by an interactive app (with either a Tcl/Tk or a shiny graphical user interface) and shiny apps with an HCL color picker and a color vision deficiency emulator. Plotting functions for displaying and assessing palettes include color swatches, visualizations of the HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation functions include: desaturation, lightening/darkening, mixing, and simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly). Details can be found on the project web page at and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical Software, ).", + "Depends": [ + "R (>= 3.0.0)", + "methods" + ], + "Imports": [ + "graphics", + "grDevices", + "stats" + ], + "Suggests": [ + "datasets", + "utils", + "KernSmooth", + "MASS", + "kernlab", + "mvtnorm", + "vcd", + "tcltk", + "shiny", + "shinyjs", + "ggplot2", + "dplyr", + "scales", + "grid", + "png", + "jpeg", + "knitr", + "rmarkdown", + "RColorBrewer", + "rcartocolor", + "scico", + "viridis", + "wesanderson" + ], + "VignetteBuilder": "knitr", + "License": "BSD_3_clause + file LICENSE", + "URL": "https://colorspace.R-Forge.R-project.org/, https://hclwizard.org/", + "BugReports": "https://colorspace.R-Forge.R-project.org/contact.html", + "LazyData": "yes", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "Ross Ihaka [aut], Paul Murrell [aut] (), Kurt Hornik [aut] (), Jason C. Fisher [aut] (), Reto Stauffer [aut] (), Claus O. Wilke [aut] (), Claire D. McWhite [aut] (), Achim Zeileis [aut, cre] ()", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN" + }, + "commonmark": { + "Package": "commonmark", + "Version": "1.9.5", + "Source": "Repository", + "Type": "Package", + "Title": "High Performance CommonMark and Github Markdown Rendering in R", + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", ,\"jeroenooms@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"John MacFarlane\", role = \"cph\", comment = \"Author of cmark\"))", + "Description": "The CommonMark specification defines a rationalized version of markdown syntax. This package uses the 'cmark' reference implementation for converting markdown text into various formats including html, latex and groff man. In addition it exposes the markdown parse tree in xml format. Also includes opt-in support for GFM extensions including tables, autolinks, and strikethrough text.", + "License": "BSD_2_clause + file LICENSE", + "URL": "https://docs.ropensci.org/commonmark/ https://ropensci.r-universe.dev/commonmark", + "BugReports": "https://github.com/r-lib/commonmark/issues", + "Suggests": [ + "curl", + "testthat", + "xml2" + ], + "RoxygenNote": "7.3.2", + "Language": "en-US", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), John MacFarlane [cph] (Author of cmark)", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, + "conflicted": { + "Package": "conflicted", + "Version": "1.2.0", + "Source": "Repository", + "Title": "An Alternative Conflict Resolution Strategy", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = c(\"aut\", \"cre\")), person(\"RStudio\", role = c(\"cph\", \"fnd\")) )", + "Description": "R's default conflict management system gives the most recently loaded package precedence. This can make it hard to detect conflicts, particularly when they arise because a package update creates ambiguity that did not previously exist. 'conflicted' takes a different approach, making every conflict an error and forcing you to choose which function to use.", + "License": "MIT + file LICENSE", + "URL": "https://conflicted.r-lib.org/, https://github.com/r-lib/conflicted", + "BugReports": "https://github.com/r-lib/conflicted/issues", + "Depends": [ + "R (>= 3.2)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "memoise", + "rlang (>= 1.0.0)" + ], + "Suggests": [ + "callr", + "covr", + "dplyr", + "Matrix", + "methods", + "pkgload", + "testthat (>= 3.0.0)", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], RStudio [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "cowplot": { + "Package": "cowplot", + "Version": "1.1.3", + "Source": "Repository", + "Title": "Streamlined Plot Theme and Plot Annotations for 'ggplot2'", + "Authors@R": "person( given = \"Claus O.\", family = \"Wilke\", role = c(\"aut\", \"cre\"), email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\") )", + "Description": "Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. The package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization.", + "URL": "https://wilkelab.org/cowplot/", + "BugReports": "https://github.com/wilkelab/cowplot/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "ggplot2 (>= 3.4.0)", + "grid", + "gtable", + "grDevices", + "methods", + "rlang", + "scales" + ], + "License": "GPL-2", + "Suggests": [ + "Cairo", + "covr", + "dplyr", + "forcats", + "gridGraphics (>= 0.4-0)", + "knitr", + "lattice", + "magick", + "maps", + "PASWR", + "patchwork", + "rmarkdown", + "ragg", + "testthat (>= 1.0.0)", + "tidyr", + "vdiffr (>= 0.3.0)", + "VennDiagram" + ], + "VignetteBuilder": "knitr", + "Collate": "'add_sub.R' 'align_plots.R' 'as_grob.R' 'as_gtable.R' 'axis_canvas.R' 'cowplot.R' 'draw.R' 'get_plot_component.R' 'get_axes.R' 'get_titles.R' 'get_legend.R' 'get_panel.R' 'gtable.R' 'key_glyph.R' 'plot_grid.R' 'save.R' 'set_null_device.R' 'setup.R' 'stamp.R' 'themes.R' 'utils_ggplot2.R'", + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Claus O. Wilke [aut, cre] ()", + "Maintainer": "Claus O. Wilke ", + "Repository": "CRAN" + }, + "cpp11": { + "Package": "cpp11", + "Version": "0.5.2", + "Source": "Repository", + "Title": "A C++11 Interface for R's C Interface", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", email = \"davis@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Jim\",\"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Benjamin\", \"Kietzman\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.", + "License": "MIT + file LICENSE", + "URL": "https://cpp11.r-lib.org, https://github.com/r-lib/cpp11", + "BugReports": "https://github.com/r-lib/cpp11/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "bench", + "brio", + "callr", + "cli", + "covr", + "decor", + "desc", + "ggplot2", + "glue", + "knitr", + "lobstr", + "mockery", + "progress", + "rmarkdown", + "scales", + "Rcpp", + "testthat (>= 3.2.0)", + "tibble", + "utils", + "vctrs", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/Needs/cpp11/cpp_register": "brio, cli, decor, desc, glue, tibble, vctrs", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Davis Vaughan [aut, cre] (), Jim Hester [aut] (), Romain François [aut] (), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "crayon": { + "Package": "crayon", + "Version": "1.5.3", + "Source": "Repository", + "Title": "Colored Terminal Output", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Brodie\", \"Gaslam\", , \"brodie.gaslam@yahoo.com\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The crayon package is now superseded. Please use the 'cli' package for new projects. Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon", + "BugReports": "https://github.com/r-lib/crayon/issues", + "Imports": [ + "grDevices", + "methods", + "utils" + ], + "Suggests": [ + "mockery", + "rstudioapi", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Collate": "'aaa-rstudio-detect.R' 'aaaa-rematch2.R' 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.R' 'ansi-palette.R' 'combine.R' 'string.R' 'utils.R' 'crayon-package.R' 'disposable.R' 'enc-utils.R' 'has_ansi.R' 'has_color.R' 'link.R' 'styles.R' 'machinery.R' 'parts.R' 'print.R' 'style-var.R' 'show.R' 'string_operations.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, + "crosstalk": { + "Package": "crosstalk", + "Version": "1.2.1", + "Source": "Repository", + "Type": "Package", + "Title": "Inter-Widget Interactivity for HTML Widgets", + "Authors@R": "c( person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@posit.co\"), person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@posit.co\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js library\"), person(\"Kristopher Michael\", \"Kowal\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(family = \"es5-shim contributors\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(\"Denis\", \"Ineshin\", role = c(\"ctb\", \"cph\"), comment = \"ion.rangeSlider library\"), person(\"Sami\", \"Samhuri\", role = c(\"ctb\", \"cph\"), comment = \"Javascript strftime library\") )", + "Description": "Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). Currently supports linked brushing and filtering.", + "License": "MIT + file LICENSE", + "Imports": [ + "htmltools (>= 0.3.6)", + "jsonlite", + "lazyeval", + "R6" + ], + "Suggests": [ + "shiny", + "ggplot2", + "testthat (>= 2.1.0)", + "sass", + "bslib" + ], + "URL": "https://rstudio.github.io/crosstalk/, https://github.com/rstudio/crosstalk", + "BugReports": "https://github.com/rstudio/crosstalk/issues", + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Joe Cheng [aut], Carson Sievert [aut, cre] (), Posit Software, PBC [cph, fnd], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Brian Reavis [ctb, cph] (selectize.js library), Kristopher Michael Kowal [ctb, cph] (es5-shim library), es5-shim contributors [ctb, cph] (es5-shim library), Denis Ineshin [ctb, cph] (ion.rangeSlider library), Sami Samhuri [ctb, cph] (Javascript strftime library)", + "Maintainer": "Carson Sievert ", + "Repository": "CRAN" + }, + "curl": { + "Package": "curl", + "Version": "6.4.0", + "Source": "Repository", + "Type": "Package", + "Title": "A Modern and Flexible Web Client for R", + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Posit Software, PBC\", role = \"cph\"))", + "Description": "Bindings to 'libcurl' for performing fully configurable HTTP/FTP requests where responses can be processed in memory, on disk, or streaming via the callback or connection interfaces. 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"Source": "Repository", + "Type": "Package", + "Title": "A 'dplyr' Back End for Databases", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Maximilian\", \"Girlich\", role = \"aut\"), person(\"Edgar\", \"Ruiz\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A 'dplyr' back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a 'DBI' back end; more advanced features require 'SQL' translation to be provided by the package author.", + "License": "MIT + file LICENSE", + "URL": "https://dbplyr.tidyverse.org/, https://github.com/tidyverse/dbplyr", + "BugReports": "https://github.com/tidyverse/dbplyr/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "blob (>= 1.2.0)", + "cli (>= 3.6.1)", + "DBI (>= 1.1.3)", + "dplyr (>= 1.1.2)", + "glue (>= 1.6.2)", + "lifecycle (>= 1.0.3)", + "magrittr", + "methods", + "pillar (>= 1.9.0)", + "purrr (>= 1.0.1)", + "R6 (>= 2.2.2)", + "rlang (>= 1.1.1)", + "tibble (>= 3.2.1)", + "tidyr (>= 1.3.0)", + "tidyselect (>= 1.2.1)", + "utils", + "vctrs (>= 0.6.3)", + "withr (>= 2.5.0)" + ], + "Suggests": [ + "bit64", + "covr", + "knitr", + "Lahman", + "nycflights13", + "odbc (>= 1.4.2)", + "RMariaDB (>= 1.2.2)", + "rmarkdown", + "RPostgres (>= 1.4.5)", + "RPostgreSQL", + "RSQLite (>= 2.3.1)", + "testthat (>= 3.1.10)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "TRUE", + "Encoding": "UTF-8", + "Language": "en-gb", + "RoxygenNote": "7.3.1", + "Collate": "'db-sql.R' 'utils-check.R' 'import-standalone-types-check.R' 'import-standalone-obj-type.R' 'utils.R' 'sql.R' 'escape.R' 'translate-sql-cut.R' 'translate-sql-quantile.R' 'translate-sql-string.R' 'translate-sql-paste.R' 'translate-sql-helpers.R' 'translate-sql-window.R' 'translate-sql-conditional.R' 'backend-.R' 'backend-access.R' 'backend-hana.R' 'backend-hive.R' 'backend-impala.R' 'verb-copy-to.R' 'backend-mssql.R' 'backend-mysql.R' 'backend-odbc.R' 'backend-oracle.R' 'backend-postgres.R' 'backend-postgres-old.R' 'backend-redshift.R' 'backend-snowflake.R' 'backend-spark-sql.R' 'backend-sqlite.R' 'backend-teradata.R' 'build-sql.R' 'data-cache.R' 'data-lahman.R' 'data-nycflights13.R' 'db-escape.R' 'db-io.R' 'db.R' 'dbplyr.R' 'explain.R' 'ident.R' 'import-standalone-s3-register.R' 'join-by-compat.R' 'join-cols-compat.R' 'lazy-join-query.R' 'lazy-ops.R' 'lazy-query.R' 'lazy-select-query.R' 'lazy-set-op-query.R' 'memdb.R' 'optimise-utils.R' 'pillar.R' 'progress.R' 'sql-build.R' 'query-join.R' 'query-select.R' 'query-semi-join.R' 'query-set-op.R' 'query.R' 'reexport.R' 'remote.R' 'rows.R' 'schema.R' 'simulate.R' 'sql-clause.R' 'sql-expr.R' 'src-sql.R' 'src_dbi.R' 'table-name.R' 'tbl-lazy.R' 'tbl-sql.R' 'test-frame.R' 'testthat.R' 'tidyeval-across.R' 'tidyeval.R' 'translate-sql.R' 'utils-format.R' 'verb-arrange.R' 'verb-compute.R' 'verb-count.R' 'verb-distinct.R' 'verb-do-query.R' 'verb-do.R' 'verb-expand.R' 'verb-fill.R' 'verb-filter.R' 'verb-group_by.R' 'verb-head.R' 'verb-joins.R' 'verb-mutate.R' 'verb-pivot-longer.R' 'verb-pivot-wider.R' 'verb-pull.R' 'verb-select.R' 'verb-set-ops.R' 'verb-slice.R' 'verb-summarise.R' 'verb-uncount.R' 'verb-window.R' 'zzz.R'", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Maximilian Girlich [aut], Edgar Ruiz [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "deldir": { + "Package": "deldir", + "Version": "2.0-4", + "Source": "Repository", + "Date": "2024-02-27", + "Title": "Delaunay Triangulation and Dirichlet (Voronoi) Tessellation", + "Author": "Rolf Turner", + "Maintainer": "Rolf Turner ", + "Depends": [ + "R (>= 3.5.0)" + ], + "Suggests": [ + "polyclip" + ], + "Imports": [ + "graphics", + "grDevices" + ], + "Description": "Calculates the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. Plots triangulations and tessellations in various ways. Clips tessellations to sub-windows. Calculates perimeters of tessellations. Summarises information about the tiles of the tessellation.\tCalculates the centroidal Voronoi (Dirichlet) tessellation using Lloyd's algorithm.", + "LazyData": "true", + "ByteCompile": "true", + "License": "GPL (>= 2)", + "NeedsCompilation": "yes", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "dendextend": { + "Package": "dendextend", + "Version": "1.19.1", + "Source": "Repository", + "Type": "Package", + "Title": "Extending 'dendrogram' Functionality in R", + "Date": "2025-07-15", + "Authors@R": "c(person(\"Tal\", \"Galili\", role = c(\"aut\", \"cre\", \"cph\"), email = \"tal.galili@gmail.com\", comment = \"https://www.r-statistics.com\"), person(\"Yoav\", \"Benjamini\", email = \"ybenja@tau.ac.il\",role = \"ths\"), person(\"Gavin\", \"Simpson\", role = \"ctb\"), person(\"Gregory\",\"Jefferis\", role = c(\"aut\", \"ctb\"), email = \"jefferis@gmail.com\", comment =\"imported code from his dendroextras package\"), person(\"Marco\", \"Gallotta\", role = \"ctb\", comment = \"a.k.a: marcog\") , person(\"Johan\", \"Renaudie\", role = \"ctb\", comment = \"https://github.com/plannapus\"), person(\"The R Core Team\", role = \"ctb\", comment = \"Thanks for the Infastructure, and code in the examples\"), person(\"Kurt\", \"Hornik\", role = \"ctb\"), person(\"Uwe\", \"Ligges\", role = \"ctb\"), person(\"Andrej-Nikolai\", \"Spiess\", role = \"ctb\"), person(\"Steve\", \"Horvath\",email = \"SHorvath@mednet.ucla.edu\", role = \"ctb\"), person(\"Peter\", \"Langfelder\",email = \"Peter.Langfelder@gmail.com\", role = \"ctb\"), person(\"skullkey\", role = \"ctb\"), person(\"Mark\", \"Van Der Loo\", email = \"mark.vanderloo@gmail.com\", comment = \"https://github.com/markvanderloo d3dendrogram\", role = \"ctb\"), person(\"Andrie\", \"de Vries\", email = \"apdevries@gmail.com\", comment = \"ggdendro author\", role = \"ctb\"), person(\"Zuguang\", \"Gu\", email = \"z.gu@dkfz-heidelberg.de\", comment = \"circlize author\", role = \"ctb\"), person(\"Cath\", comment = \"https://github.com/CathG\", role = \"ctb\"), person(\"John\", \"Ma\", comment = \"https://github.com/JohnMCMa\", role = \"ctb\"), person(\"Krzysiek\", \"G\", comment = \"https://github.com/storaged\", role = \"ctb\"), person(\"Manuela\", \"Hummel\", email = \"m.hummel@dkfz.de\", comment = \"https://github.com/hummelma\", role = \"ctb\"), person(\"Chase\", \"Clark\", comment = \"https://github.com/chasemc\", role = \"ctb\"), person(\"Lucas\", \"Graybuck\", comment = \"https://github.com/hypercompetent\", role = \"ctb\"), person(\"jdetribol\", comment = \"https://github.com/jdetribol\", role = \"ctb\"), person(\"Ben\", \"Ho\", role = \"ctb\", email = \"ben.ho@sickkids.ca\", comment = \"https://github.com/SplitInf\"), person(\"Samuel\", \"Perreault\", role = \"ctb\", email = \"samuel.perreault.3@ulaval.ca\", comment = \"https://github.com/samperochkin\"), person(\"Christian\", \"Hennig\", role = \"ctb\", email = \"c.hennig@ucl.ac.uk\", comment = \"http://www.homepages.ucl.ac.uk/~ucakche/\"), person(\"David\", \"Bradley\", role = \"ctb\", comment = \"https://github.com/DBradley27\"), person(\"Houyun\", \"Huang\", role = \"ctb\", email = 'houyunhuang@163.com', comment = \"https://github.com/houyunhuang\"), person(\"Patrick\", \"Schupp\", role = \"ctb\", email = 'pschupp@sonic.net', comment = \"https://github.com/pschupp\"), person(\"Alec\", \"Buetow\", role = \"ctb\", email = 'alecbuetow@gmail.com', comment = \"https://github.com/alecbuetow\") )", + "Description": "Offers a set of functions for extending 'dendrogram' objects in R, letting you visualize and compare trees of 'hierarchical clusterings'. 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(2) Visually and statistically compare different 'dendrograms' to one another.", + "Depends": [ + "R (>= 3.0.0)" + ], + "Imports": [ + "utils", + "stats", + "datasets", + "magrittr (>= 1.0.1)", + "ggplot2", + "viridis" + ], + "Suggests": [ + "knitr", + "rmarkdown", + "testthat", + "seriation", + "colorspace", + "ape", + "microbenchmark", + "gplots", + "heatmaply", + "dynamicTreeCut", + "pvclust", + "corrplot", + "DendSer", + "MASS", + "cluster", + "fpc", + "circlize (>= 0.2.5)", + "covr" + ], + "Enhances": [ + "ggdendro", + "dendroextras", + "Hmisc", + "data.table", + "rpart", + "WGCNA", + "moduleColor", + "distory", + "phangorn", + "zoo" + ], + "VignetteBuilder": "knitr", + "LazyData": "true", + "License": "GPL-2 | GPL-3", + "URL": "https://talgalili.github.io/dendextend/, https://github.com/talgalili/dendextend/, https://cran.r-project.org/package=dendextend, https://www.r-statistics.com/tag/dendextend/, https://doi.org/10.1093/bioinformatics/btv428", + "BugReports": 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Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.", + "URL": "https://github.com/eddelbuettel/digest, https://dirk.eddelbuettel.com/code/digest.html", + "BugReports": "https://github.com/eddelbuettel/digest/issues", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "utils" + ], + "License": "GPL (>= 2)", + "Suggests": [ + "tinytest", + "simplermarkdown" + ], + "VignetteBuilder": "simplermarkdown", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (), Antoine Lucas [ctb], Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (), Simon Urbanek [ctb] (), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb], Duncan Murdoch [ctb], Jim Hester [ctb], Wush Wu [ctb] (), Qiang Kou [ctb] (), Thierry Onkelinx [ctb] (), Michel Lang [ctb] (), Viliam Simko [ctb], Kurt Hornik [ctb] (), Radford Neal [ctb] 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Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models, quasi-likelihood, and gene set enrichment. Can perform differential analyses of any type of omics data that produces read counts, including RNA-seq, ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE, CAGE, metabolomics, or proteomics spectral counts. RNA-seq analyses can be conducted at the gene or isoform level, and tests can be conducted for differential exon or transcript usage.", + "Author": "Yunshun Chen, Lizhong Chen, Aaron TL Lun, Davis J McCarthy, Pedro Baldoni, Matthew E Ritchie, Belinda Phipson, Yifang Hu, Xiaobei Zhou, Mark D Robinson, Gordon K Smyth", + "Maintainer": "Yunshun Chen , Gordon Smyth , Aaron Lun , Mark Robinson ", + "License": "GPL (>=2)", + "Depends": [ + "R (>= 3.6.0)", + "limma (>= 3.63.6)" + ], + "Imports": [ + "methods", + "graphics", + "stats", + "utils", + "locfit" + ], + "Suggests": [ + "arrow", + "jsonlite", + "knitr", + "Matrix", + "readr", + "rhdf5", + "SeuratObject", + "splines", + "AnnotationDbi", + "Biobase", + "BiocStyle", + "org.Hs.eg.db", + "SummarizedExperiment" + ], + "VignetteBuilder": "knitr", + "URL": "https://bioinf.wehi.edu.au/edgeR/, https://bioconductor.org/packages/edgeR", + "biocViews": "AlternativeSplicing, BatchEffect, Bayesian, BiomedicalInformatics, CellBiology, ChIPSeq, Clustering, Coverage, DifferentialExpression, DifferentialMethylation, DifferentialSplicing, DNAMethylation, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, Genetics, ImmunoOncology, MultipleComparison, Normalization, Pathways, Proteomics, QualityControl, Regression, RNASeq, SAGE, Sequencing, SingleCell, SystemsBiology, TimeCourse, Transcription, Transcriptomics", + "NeedsCompilation": "yes", + "git_url": "https://git.bioconductor.org/packages/edgeR", + "git_branch": "RELEASE_3_21", + "git_last_commit": "0dc836a", + "git_last_commit_date": "2025-07-04", + "Repository": "Bioconductor 3.21" + }, + "emmeans": { + "Package": "emmeans", + "Version": "1.11.2", + "Source": "Repository", + "Type": "Package", + "Title": "Estimated Marginal Means, aka Least-Squares Means", + "Date": "2025-07-11", + "Authors@R": "c(person(\"Russell V.\", \"Lenth\", role = c(\"aut\", \"cre\", \"cph\"), email = \"russell-lenth@uiowa.edu\"), person(\"Balazs\", \"Banfai\", role = \"ctb\"), person(\"Ben\", \"Bolker\", role = \"ctb\"), person(\"Paul\", \"Buerkner\", role = \"ctb\"), person(\"Iago\", \"Giné-Vázquez\", role = \"ctb\"), person(\"Maxime\", \"Herve\", role = \"ctb\"), person(\"Maarten\", \"Jung\", role = \"ctb\"), person(\"Jonathon\", \"Love\", role = \"ctb\"), person(\"Fernando\", \"Miguez\", role = \"ctb\"), person(\"Julia\", \"Piaskowski\", role = \"ctb\"), person(\"Hannes\", \"Riebl\", role = \"ctb\"), person(\"Henrik\", \"Singmann\", role = \"ctb\"))", + "Depends": [ + "R (>= 4.1.0)" + ], + "Imports": [ + "estimability (>= 1.4.1)", + "graphics", + "methods", + "mvtnorm", + "numDeriv", + "stats", + "utils" + ], + "Suggests": [ + "bayesplot", + "bayestestR", + "biglm", + "brms", + "car", + "coda (>= 0.17)", + "compositions", + "ggplot2", + "knitr", + "lattice", + "lme4", + "lmerTest (>= 2.0.32)", + "logspline", + "MASS", + "mediation", + "mgcv", + "multcomp", + "multcompView", + "MuMIn", + "nlme", + "ordinal (>= 2014.11-12)", + "pbkrtest (>= 0.4-1)", + "rmarkdown", + "rsm", + "sandwich", + "scales", + "splines", + "testthat", + "tibble", + "xtable (>= 1.8-2)" + ], + "Enhances": [ + "CARBayes", + "coxme", + "gee", + "geepack", + "MCMCglmm", + "MCMCpack", + "mice", + "nnet", + "pscl", + "rstanarm", + "sommer", + "survival" + ], + "URL": "https://rvlenth.github.io/emmeans/,https://rvlenth.github.io/emmeans/", + "BugReports": "https://github.com/rvlenth/emmeans/issues", + "LazyData": "yes", + "ByteCompile": "yes", + "Description": "Obtain estimated marginal means (EMMs) for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays. Least-squares means are discussed, and the term \"estimated marginal means\" is suggested, in Searle, Speed, and Milliken (1980) Population marginal means in the linear model: An alternative to least squares means, The American Statistician 34(4), 216-221 .", + "License": "GPL-2 | GPL-3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "VignetteBuilder": "knitr", + "NeedsCompilation": "no", + "Author": "Russell V. Lenth [aut, cre, cph], Balazs Banfai [ctb], Ben Bolker [ctb], Paul Buerkner [ctb], Iago Giné-Vázquez [ctb], Maxime Herve [ctb], Maarten Jung [ctb], Jonathon Love [ctb], Fernando Miguez [ctb], Julia Piaskowski [ctb], Hannes Riebl [ctb], Henrik Singmann [ctb]", + "Maintainer": "Russell V. Lenth ", + "Repository": "CRAN" + }, + "estimability": { + "Package": "estimability", + "Version": "1.5.1", + "Source": "Repository", + "Type": "Package", + "Title": "Tools for Assessing Estimability of Linear Predictions", + "Date": "2024-05-12", + "Authors@R": "c(person(\"Russell\", \"Lenth\", role = c(\"aut\", \"cre\", \"cph\"), email = \"russell-lenth@uiowa.edu\"))", + "Depends": [ + "stats", + "R(>= 4.1.0)" + ], + "Suggests": [ + "knitr", + "rmarkdown" + ], + "Description": "Provides tools for determining estimability of linear functions of regression coefficients, and 'epredict' methods that handle non-estimable cases correctly. 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As different colour spaces have different uses, efficient conversion between these representations are important. The 'farver' package provides a set of functions that gives access to very fast colour space conversion and comparisons implemented in C++, and offers speed improvements over the 'convertColor' function in the 'grDevices' package.", + "License": "MIT + file LICENSE", + "URL": "https://farver.data-imaginist.com, https://github.com/thomasp85/farver", + "BugReports": "https://github.com/thomasp85/farver/issues", + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "Thomas Lin Pedersen [cre, aut] (), Berendea Nicolae [aut] (Author of the ColorSpace C++ library), Romain François [aut] (), Posit, PBC [cph, fnd]", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "CRAN" + }, + "fastDummies": { + "Package": "fastDummies", + "Version": "1.7.5", + "Source": "Repository", + "Type": "Package", + "Title": "Fast Creation of Dummy (Binary) Columns and Rows from Categorical Variables", + "Authors@R": "c( person(\"Jacob\", \"Kaplan\", email = \"jkkaplan6@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0601-0387\")), person(\"Benjamin\", \"Schlegel\", email = \"kontakt@benjaminschlegl.ch\", role = \"ctb\"))", + "Description": "Creates dummy columns from columns that have categorical variables (character or factor types). You can also specify which columns to make dummies out of, or which columns to ignore. Also creates dummy rows from character, factor, and Date columns. This package provides a significant speed increase from creating dummy variables through model.matrix().", + "Depends": [ + "R (>= 2.10)" + ], + "Imports": [ + "data.table", + "tibble", + "stringr" + ], + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "URL": "https://github.com/jacobkap/fastDummies, https://jacobkap.github.io/fastDummies/", + "BugReports": "https://github.com/jacobkap/fastDummies/issues", + "RoxygenNote": "7.3.2", + "Suggests": [ + "testthat (>= 2.1.0)", + "knitr", + "rmarkdown", + "covr", + "spelling" + ], + "VignetteBuilder": "knitr", + "Language": "en-US", + "NeedsCompilation": "no", + "Author": "Jacob Kaplan [aut, cre] (), Benjamin Schlegel [ctb]", + "Maintainer": "Jacob Kaplan ", + "Repository": "CRAN" + }, + "fastmap": { + "Package": "fastmap", + "Version": "1.2.0", + "Source": "Repository", + "Title": "Fast Data Structures", + "Authors@R": "c( person(\"Winston\", \"Chang\", email = \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(given = \"Tessil\", role = \"cph\", comment = \"hopscotch_map library\") )", + "Description": "Fast implementation of data structures, including a key-value store, stack, and queue. Environments are commonly used as key-value stores in R, but every time a new key is used, it is added to R's global symbol table, causing a small amount of memory leakage. This can be problematic in cases where many different keys are used. Fastmap avoids this memory leak issue by implementing the map using data structures in C++.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "Suggests": [ + "testthat (>= 2.1.1)" + ], + "URL": "https://r-lib.github.io/fastmap/, https://github.com/r-lib/fastmap", + "BugReports": "https://github.com/r-lib/fastmap/issues", + "NeedsCompilation": "yes", + "Author": "Winston Chang [aut, cre], Posit Software, PBC [cph, fnd], Tessil [cph] (hopscotch_map library)", + "Maintainer": "Winston Chang ", + "Repository": "CRAN" + }, + "fitdistrplus": { + "Package": "fitdistrplus", + "Version": "1.2-4", + "Source": "Repository", + "Title": "Help to Fit of a Parametric Distribution to Non-Censored or Censored Data", + "Authors@R": "c(person(\"Marie-Laure\", \"Delignette-Muller\", role = \"aut\", email = \"marielaure.delignettemuller@vetagro-sup.fr\", comment = c(ORCID = \"0000-0001-5453-3994\")), person(\"Christophe\", \"Dutang\", role = \"aut\", email = \"christophe.dutang@ensimag.fr\", comment = c(ORCID = \"0000-0001-6732-1501\")), person(\"Regis\", \"Pouillot\", role = \"ctb\"), person(\"Jean-Baptiste\", \"Denis\", role = \"ctb\"), person(\"Aurélie\", \"Siberchicot\", role = c(\"aut\", \"cre\"), email = \"aurelie.siberchicot@univ-lyon1.fr\", comment = c(ORCID = \"0000-0002-7638-8318\")))", + "Description": "Extends the fitdistr() function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME), maximum goodness-of-fit estimation (MGE) and maximum spacing estimation (MSE) methods (available only for non-censored data). Weighted versions of MLE, MME, QME and MSE are available. See e.g. Casella & Berger (2002), Statistical inference, Pacific Grove, for a general introduction to parametric estimation.", + "Depends": [ + "R (>= 3.5.0)", + "MASS", + "grDevices", + "survival", + "methods" + ], + "Imports": [ + "stats", + "rlang" + ], + "Suggests": [ + "actuar", + "rgenoud", + "mc2d", + "gamlss.dist", + "knitr", + "ggplot2", + "GeneralizedHyperbolic", + "rmarkdown", + "Hmisc", + "bookdown" + ], + "VignetteBuilder": "knitr", + "BuildVignettes": "true", + "License": "GPL (>= 2)", + "Encoding": "UTF-8", + "URL": "https://lbbe-software.github.io/fitdistrplus/, https://lbbe.univ-lyon1.fr/fr/fitdistrplus, https://github.com/lbbe-software/fitdistrplus", + "BugReports": "https://github.com/lbbe-software/fitdistrplus/issues", + "Contact": "Marie-Laure Delignette-Muller or Christophe Dutang ", + "NeedsCompilation": "no", + "Author": "Marie-Laure Delignette-Muller [aut] (ORCID: ), Christophe Dutang [aut] (ORCID: ), Regis Pouillot [ctb], Jean-Baptiste Denis [ctb], Aurélie Siberchicot [aut, cre] (ORCID: )", + "Maintainer": "Aurélie Siberchicot ", + "Repository": "CRAN" + }, + "fontawesome": { + "Package": "fontawesome", + "Version": "0.5.3", + "Source": "Repository", + "Type": "Package", + "Title": "Easily Work with 'Font Awesome' Icons", + "Description": "Easily and flexibly insert 'Font Awesome' icons into 'R Markdown' documents and 'Shiny' apps. These icons can be inserted into HTML content through inline 'SVG' tags or 'i' tags. There is also a utility function for exporting 'Font Awesome' icons as 'PNG' images for those situations where raster graphics are needed.", + "Authors@R": "c( person(\"Richard\", \"Iannone\", , \"rich@posit.co\", c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-3925-190X\")), person(\"Christophe\", \"Dervieux\", , \"cderv@posit.co\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = \"ctb\"), person(\"Dave\", \"Gandy\", role = c(\"ctb\", \"cph\"), comment = \"Font-Awesome font\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "License": "MIT + file LICENSE", + "URL": "https://github.com/rstudio/fontawesome, https://rstudio.github.io/fontawesome/", + "BugReports": "https://github.com/rstudio/fontawesome/issues", + "Encoding": "UTF-8", + "ByteCompile": "true", + "RoxygenNote": "7.3.2", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "rlang (>= 1.0.6)", + "htmltools (>= 0.5.1.1)" + ], + "Suggests": [ + "covr", + "dplyr (>= 1.0.8)", + "gt (>= 0.9.0)", + "knitr (>= 1.31)", + "testthat (>= 3.0.0)", + "rsvg" + ], + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "Richard Iannone [aut, cre] (), Christophe Dervieux [ctb] (), Winston Chang [ctb], Dave Gandy [ctb, cph] (Font-Awesome font), Posit Software, PBC [cph, fnd]", + "Maintainer": "Richard Iannone ", + "Repository": "CRAN" + }, + "forcats": { + "Package": "forcats", + "Version": "1.0.0", + "Source": "Repository", + "Title": "Tools for Working with Categorical Variables (Factors)", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = c(\"aut\", \"cre\")), person(\"RStudio\", role = c(\"cph\", \"fnd\")) )", + "Description": "Helpers for reordering factor levels (including moving specified levels to front, ordering by first appearance, reversing, and randomly shuffling), and tools for modifying factor levels (including collapsing rare levels into other, 'anonymising', and manually 'recoding').", + "License": "MIT + file LICENSE", + "URL": "https://forcats.tidyverse.org/, https://github.com/tidyverse/forcats", + "BugReports": "https://github.com/tidyverse/forcats/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "glue", + "lifecycle", + "magrittr", + "rlang (>= 1.0.0)", + "tibble" + ], + "Suggests": [ + "covr", + "dplyr", + "ggplot2", + "knitr", + "readr", + "rmarkdown", + "testthat (>= 3.0.0)", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], RStudio [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "foreach": { + "Package": "foreach", + "Version": "1.5.2", + "Source": "Repository", + "Type": "Package", + "Title": "Provides Foreach Looping Construct", + "Authors@R": "c(person(\"Folashade\", \"Daniel\", role=\"cre\", email=\"fdaniel@microsoft.com\"), person(\"Hong\", \"Ooi\", role=\"ctb\"), person(\"Rich\", \"Calaway\", role=\"ctb\"), person(\"Microsoft\", role=c(\"aut\", \"cph\")), person(\"Steve\", \"Weston\", role=\"aut\"))", + "Description": "Support for the foreach looping construct. Foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. This package in particular is intended to be used for its return value, rather than for its side effects. In that sense, it is similar to the standard lapply function, but doesn't require the evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel.", + "License": "Apache License (== 2.0)", + "URL": "https://github.com/RevolutionAnalytics/foreach", + "BugReports": "https://github.com/RevolutionAnalytics/foreach/issues", + "Depends": [ + "R (>= 2.5.0)" + ], + "Imports": [ + "codetools", + "utils", + "iterators" + ], + "Suggests": [ + "randomForest", + "doMC", + "doParallel", + "testthat", + "knitr", + "rmarkdown" + ], + "VignetteBuilder": "knitr", + "RoxygenNote": "7.1.1", + "Collate": "'callCombine.R' 'foreach.R' 'do.R' 'foreach-ext.R' 'foreach-pkg.R' 'getDoPar.R' 'getDoSeq.R' 'getsyms.R' 'iter.R' 'nextElem.R' 'onLoad.R' 'setDoPar.R' 'setDoSeq.R' 'times.R' 'utils.R'", + "NeedsCompilation": "no", + "Author": "Folashade Daniel [cre], Hong Ooi [ctb], Rich Calaway [ctb], Microsoft [aut, cph], Steve Weston [aut]", + "Maintainer": "Folashade Daniel ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "foreign": { + "Package": "foreign", + "Version": "0.8-90", + "Source": "Repository", + "Priority": "recommended", + "Date": "2025-03-31", + "Title": "Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', 'dBase', ...", + "Depends": [ + "R (>= 4.0.0)" + ], + "Imports": [ + "methods", + "utils", + "stats" + ], + "Authors@R": "c( person(\"R Core Team\", email = \"R-core@R-project.org\", role = c(\"aut\", \"cph\", \"cre\"), comment = c(ROR = \"02zz1nj61\")), person(\"Roger\", \"Bivand\", role = c(\"ctb\", \"cph\")), person(c(\"Vincent\", \"J.\"), \"Carey\", role = c(\"ctb\", \"cph\")), person(\"Saikat\", \"DebRoy\", role = c(\"ctb\", \"cph\")), person(\"Stephen\", \"Eglen\", role = c(\"ctb\", \"cph\")), person(\"Rajarshi\", \"Guha\", role = c(\"ctb\", \"cph\")), person(\"Swetlana\", \"Herbrandt\", role = \"ctb\"), person(\"Nicholas\", \"Lewin-Koh\", role = c(\"ctb\", \"cph\")), person(\"Mark\", \"Myatt\", role = c(\"ctb\", \"cph\")), person(\"Michael\", \"Nelson\", role = \"ctb\"), person(\"Ben\", \"Pfaff\", role = \"ctb\"), person(\"Brian\", \"Quistorff\", role = \"ctb\"), person(\"Frank\", \"Warmerdam\", role = c(\"ctb\", \"cph\")), person(\"Stephen\", \"Weigand\", role = c(\"ctb\", \"cph\")), person(\"Free Software Foundation, Inc.\", role = \"cph\"))", + "Contact": "see 'MailingList'", + "Copyright": "see file COPYRIGHTS", + "Description": "Reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files.", + "ByteCompile": "yes", + "Biarch": "yes", + "License": "GPL (>= 2)", + "BugReports": "https://bugs.r-project.org", + "MailingList": "R-help@r-project.org", + "URL": "https://svn.r-project.org/R-packages/trunk/foreign/", + "NeedsCompilation": "yes", + "Author": "R Core Team [aut, cph, cre] (02zz1nj61), Roger Bivand [ctb, cph], Vincent J. 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\"0000-0002-6983-2759\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Interact with Google Sheets through the Sheets API v4 . \"API\" is an acronym for \"application programming interface\"; the Sheets API allows users to interact with Google Sheets programmatically, instead of via a web browser. The \"v4\" refers to the fact that the Sheets API is currently at version 4. 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Warnes [aut], Ben Bolker [aut], Lodewijk Bonebakker [aut], Robert Gentleman [aut], Wolfgang Huber [aut], Andy Liaw [aut], Thomas Lumley [aut], Martin Maechler [aut], Arni Magnusson [aut], Steffen Moeller [aut], Marc Schwartz [aut], Bill Venables [aut], Tal Galili [aut, cre]", + "Maintainer": "Tal Galili ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "grafify": { + "Package": "grafify", + "Version": "5.0.0.1", + "Source": "Repository", + "Type": "Package", + "Title": "Easy Graphs for Data Visualisation and Linear Models for ANOVA", + "Date": "2025-03-10", + "Authors@R": "c(person(\"Avinash R\", \"Shenoy\", email = \"a.shenoy@imperial.ac.uk\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0001-6228-9303\")))", + "Description": "Easily explore data by plotting graphs with a few lines of code. Use these ggplot() wrappers to quickly draw graphs of scatter/dots with box-whiskers, violins or SD error bars, data distributions, before-after graphs, factorial ANOVA and more. 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The 'gtable' package defines a 'gtable' grob class that specifies a grid along with a list of grobs and their placement in the grid. 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Declare the relative path of a file within your project with 'i_am()'. Use the 'here()' function as a drop-in replacement for 'file.path()', it will always locate the files relative to your project root.", + "License": "MIT + file LICENSE", + "URL": "https://here.r-lib.org/, https://github.com/r-lib/here", + "BugReports": "https://github.com/r-lib/here/issues", + "Imports": [ + "rprojroot (>= 2.0.2)" + ], + "Suggests": [ + "conflicted", + "covr", + "fs", + "knitr", + "palmerpenguins", + "plyr", + "readr", + "rlang", + "rmarkdown", + "testthat", + "uuid", + "withr" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.1.1.9000", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "Kirill Müller [aut, cre] (), Jennifer Bryan [ctb] ()", + "Maintainer": "Kirill Müller ", + "Repository": "CRAN" + }, + "highr": { + "Package": "highr", + "Version": "0.11", + "Source": "Repository", + "Type": "Package", + "Title": "Syntax Highlighting for R Source Code", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Yixuan\", \"Qiu\", role = \"aut\"), person(\"Christopher\", \"Gandrud\", role = \"ctb\"), person(\"Qiang\", \"Li\", role = \"ctb\") )", + "Description": "Provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package ().", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "xfun (>= 0.18)" + ], + "Suggests": [ + "knitr", + "markdown", + "testit" + ], + "License": "GPL", + "URL": "https://github.com/yihui/highr", + "BugReports": "https://github.com/yihui/highr/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre] (), Yixuan Qiu [aut], Christopher Gandrud [ctb], Qiang Li [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" + }, + "hms": { + "Package": "hms", + "Version": "1.1.3", + "Source": "Repository", + "Title": "Pretty Time of Day", + "Date": "2023-03-21", + "Authors@R": "c( person(\"Kirill\", \"Müller\", role = c(\"aut\", \"cre\"), email = \"kirill@cynkra.com\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"R Consortium\", role = \"fnd\"), person(\"RStudio\", role = \"fnd\") )", + "Description": "Implements an S3 class for storing and formatting time-of-day values, based on the 'difftime' class.", + "Imports": [ + "lifecycle", + "methods", + "pkgconfig", + "rlang (>= 1.0.2)", + "vctrs (>= 0.3.8)" + ], + "Suggests": [ + "crayon", + "lubridate", + "pillar (>= 1.1.0)", + "testthat (>= 3.0.0)" + ], + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "URL": "https://hms.tidyverse.org/, https://github.com/tidyverse/hms", + "BugReports": "https://github.com/tidyverse/hms/issues", + "RoxygenNote": "7.2.3", + "Config/testthat/edition": "3", + "Config/autostyle/scope": "line_breaks", + "Config/autostyle/strict": "false", + "Config/Needs/website": "tidyverse/tidytemplate", + "NeedsCompilation": "no", + "Author": "Kirill Müller [aut, cre] (), R Consortium [fnd], RStudio [fnd]", + "Maintainer": "Kirill Müller ", + "Repository": "CRAN" + }, + "htmlTable": { + "Package": "htmlTable", + "Version": "2.4.3", + "Source": "Repository", + "Title": "Advanced Tables for Markdown/HTML", + "Authors@R": "c( person(\"Max\", \"Gordon\", email = \"max@gforge.se\", role = c(\"aut\", \"cre\")), person(\"Stephen\", \"Gragg\", role=c(\"aut\")), person(\"Peter\", \"Konings\", role=c(\"aut\")))", + "Maintainer": "Max Gordon ", + "Description": "Tables with state-of-the-art layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying css-structure is simple in order to maximize compatibility with common word processors. The package also contains a few text formatting functions that help outputting text compatible with HTML/LaTeX.", + "License": "GPL (>= 3)", + "URL": "https://gforge.se/packages/", + "BugReports": "https://github.com/gforge/htmlTable/issues", + "Biarch": "yes", + "Depends": [ + "R (>= 4.1)" + ], + "Imports": [ + "stringr", + "knitr (>= 1.6)", + "magrittr (>= 1.5)", + "methods", + "checkmate", + "htmlwidgets", + "htmltools", + "rstudioapi (>= 0.6)" + ], + "Suggests": [ + "testthat", + "XML", + "xml2", + "Hmisc", + "rmarkdown", + "chron", + "lubridate", + "tibble", + "purrr", + "tidyselect", + "glue", + "rlang", + "tidyr (>= 0.7.2)", + "dplyr (>= 0.7.4)" + ], + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "VignetteBuilder": "knitr", + "RoxygenNote": "7.2.2", + "Author": "Max Gordon [aut, cre], Stephen Gragg [aut], Peter Konings [aut]", + "Repository": "CRAN" + }, + "htmltools": { + "Package": "htmltools", + "Version": "0.5.8.1", + "Source": "Repository", + "Type": "Package", + 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It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)", + "License": "GPL (>= 2) | file LICENSE", + "URL": "https://github.com/rstudio/httpuv", + "BugReports": "https://github.com/rstudio/httpuv/issues", + "Depends": [ + "R (>= 2.15.1)" + ], + "Imports": [ + "later (>= 0.8.0)", + "promises", + "R6", + "Rcpp (>= 1.0.7)", + "utils" + ], + "Suggests": [ + "callr", + "curl", + "jsonlite", + "testthat", + "websocket" + ], + "LinkingTo": [ + "later", + "Rcpp" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "SystemRequirements": "GNU make, zlib", + "Collate": "'RcppExports.R' 'httpuv.R' 'random_port.R' 'server.R' 'staticServer.R' 'static_paths.R' 'utils.R'", + "NeedsCompilation": "yes", + "Author": "Joe Cheng [aut], Winston Chang [aut, cre], Posit, PBC fnd [cph], Hector Corrada Bravo [ctb], Jeroen Ooms [ctb], Andrzej Krzemienski [cph] (optional.hpp), libuv project contributors [cph] (libuv library, see src/libuv/AUTHORS file), Joyent, Inc. and other Node contributors [cph] (libuv library, see src/libuv/AUTHORS file; and http-parser library, see src/http-parser/AUTHORS file), Niels Provos [cph] (libuv subcomponent: tree.h), Internet Systems Consortium, Inc. [cph] (libuv subcomponent: inet_pton and inet_ntop, contained in src/libuv/src/inet.c), Alexander Chemeris [cph] (libuv subcomponent: stdint-msvc2008.h (from msinttypes)), Google, Inc. [cph] (libuv subcomponent: pthread-fixes.c), Sony Mobile Communcations AB [cph] (libuv subcomponent: pthread-fixes.c), Berkeley Software Design Inc. [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Kenneth MacKay [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Emergya (Cloud4all, FP7/2007-2013, grant agreement no 289016) [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Steve Reid [aut] (SHA-1 implementation), James Brown [aut] (SHA-1 implementation), Bob Trower [aut] (base64 implementation), Alexander Peslyak [aut] (MD5 implementation), Trantor Standard Systems [cph] (base64 implementation), Igor Sysoev [cph] (http-parser)", + "Maintainer": "Winston Chang ", + "Repository": "CRAN" + }, + "httr": { + "Package": "httr", + "Version": "1.4.7", + "Source": "Repository", + "Title": "Tools for Working with URLs and HTTP", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).", + "License": "MIT + file LICENSE", + "URL": "https://httr.r-lib.org/, https://github.com/r-lib/httr", + "BugReports": "https://github.com/r-lib/httr/issues", + "Depends": [ + "R (>= 3.5)" + ], + "Imports": [ + "curl (>= 5.0.2)", + "jsonlite", + "mime", + "openssl (>= 0.8)", + "R6" + ], + "Suggests": [ + "covr", + "httpuv", + "jpeg", + "knitr", + "png", + "readr", + "rmarkdown", + "testthat (>= 0.8.0)", + "xml2" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Posit, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "ica": { + "Package": "ica", + "Version": "1.0-3", + "Source": "Repository", + "Type": "Package", + "Title": "Independent Component Analysis", + "Date": "2022-07-08", + "Author": "Nathaniel E. 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Log-likelihoods for multivariate Gaussian models and Gaussian copulae parameterised by Cholesky factors of covariance or precision matrices are implemented for interval-censored and exact data, or a mix thereof. Score functions for these log-likelihoods are available. A class representing multiple lower triangular matrices and corresponding methods are part of this package.", + "Imports": [ + "stats" + ], + "Depends": [ + "R(>= 3.5.0)" + ], + "Suggests": [ + "qrng", + "numDeriv" + ], + "License": "GPL-2", + "URL": "http://mvtnorm.R-forge.R-project.org", + "NeedsCompilation": "yes", + "Author": "Alan Genz [aut], Frank Bretz [aut], Tetsuhisa Miwa [aut], Xuefei Mi [aut], Friedrich Leisch [ctb], Fabian Scheipl [ctb], Bjoern Bornkamp [ctb] (), Martin Maechler [ctb] (), Torsten Hothorn [aut, cre] ()", + "Maintainer": "Torsten Hothorn ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "nlme": { + "Package": "nlme", + "Version": "3.1-168", + "Source": "Repository", + "Date": "2025-03-31", + "Priority": "recommended", + "Title": "Linear and Nonlinear Mixed Effects Models", + "Authors@R": "c(person(\"José\", \"Pinheiro\", role = \"aut\", comment = \"S version\"), person(\"Douglas\", \"Bates\", role = \"aut\", comment = \"up to 2007\"), person(\"Saikat\", \"DebRoy\", role = \"ctb\", comment = \"up to 2002\"), person(\"Deepayan\", \"Sarkar\", role = \"ctb\", comment = \"up to 2005\"), person(\"EISPACK authors\", role = \"ctb\", comment = \"src/rs.f\"), person(\"Siem\", \"Heisterkamp\", role = \"ctb\", comment = \"Author fixed sigma\"), person(\"Bert\", \"Van Willigen\",role = \"ctb\", comment = \"Programmer fixed sigma\"), person(\"Johannes\", \"Ranke\", role = \"ctb\", comment = \"varConstProp()\"), person(\"R Core Team\", email = \"R-core@R-project.org\", role = c(\"aut\", \"cre\"), comment = c(ROR = \"02zz1nj61\")))", + "Contact": "see 'MailingList'", + "Description": "Fit and compare Gaussian linear and nonlinear mixed-effects models.", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "graphics", + "stats", + "utils", + "lattice" + ], + "Suggests": [ + "MASS", + "SASmixed" + ], + "LazyData": "yes", + "Encoding": "UTF-8", + "License": "GPL (>= 2)", + "BugReports": "https://bugs.r-project.org", + "MailingList": "R-help@r-project.org", + "URL": "https://svn.r-project.org/R-packages/trunk/nlme/", + "NeedsCompilation": "yes", + "Author": "José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), Johannes Ranke [ctb] (varConstProp()), R Core Team [aut, cre] (02zz1nj61)", + "Maintainer": "R Core Team ", + "Repository": "CRAN" + }, + "nloptr": { + "Package": "nloptr", + "Version": "2.2.1", + "Source": "Repository", + "Type": "Package", + "Title": "R Interface to NLopt", + "Authors@R": "c(person(\"Jelmer\", \"Ypma\", role = \"aut\", email = \"uctpjyy@ucl.ac.uk\"), person(c(\"Steven\", \"G.\"), \"Johnson\", role = \"aut\", comment = \"author of the NLopt C library\"), person(\"Aymeric\", \"Stamm\", role = c(\"ctb\", \"cre\"), email = \"aymeric.stamm@cnrs.fr\", comment = c(ORCID = \"0000-0002-8725-3654\")), person(c(\"Hans\", \"W.\"), \"Borchers\", role = \"ctb\", email = \"hwborchers@googlemail.com\"), person(\"Dirk\", \"Eddelbuettel\", role = \"ctb\", email = \"edd@debian.org\"), person(\"Brian\", \"Ripley\", role = \"ctb\", comment = \"build process on multiple OS\"), person(\"Kurt\", \"Hornik\", role = \"ctb\", comment = \"build process on multiple OS\"), person(\"Julien\", \"Chiquet\", role = \"ctb\"), person(\"Avraham\", \"Adler\", role = \"ctb\", email = \"Avraham.Adler@gmail.com\", comment = c(ORCID = \"0000-0002-3039-0703\")), person(\"Xiongtao\", \"Dai\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\", email = \"jeroen@berkeley.edu\"), person(\"Tomas\", \"Kalibera\", role = \"ctb\"), person(\"Mikael\", \"Jagan\", role = \"ctb\"))", + "Description": "Solve optimization problems using an R interface to NLopt. NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. See for more information on the available algorithms. Building from included sources requires 'CMake'. On Linux and 'macOS', if a suitable system build of NLopt (2.7.0 or later) is found, it is used; otherwise, it is built from included sources via 'CMake'. 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Accurate calculations are done using 'Richardson''s' extrapolation or, when applicable, a complex step derivative is available. A simple difference method is also provided. Simple difference is (usually) less accurate but is much quicker than 'Richardson''s' extrapolation and provides a useful cross-check. Methods are provided for real scalar and vector valued functions.", + "Depends": [ + "R (>= 2.11.1)" + ], + "LazyLoad": "yes", + "ByteCompile": "yes", + "License": "GPL-2", + "Copyright": "2006-2011, Bank of Canada. 2012-2016, Paul Gilbert", + "Author": "Paul Gilbert and Ravi Varadhan", + "Maintainer": "Paul Gilbert ", + "URL": "http://optimizer.r-forge.r-project.org/", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, + "openssl": { + "Package": "openssl", + "Version": "2.3.3", + "Source": "Repository", + "Type": "Package", + "Title": "Toolkit for Encryption, Signatures and Certificates Based on OpenSSL", + "Authors@R": "c(person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Oliver\", \"Keyes\", role = \"ctb\"))", + "Description": "Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers. Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.", + "License": "MIT + file LICENSE", + "URL": "https://jeroen.r-universe.dev/openssl", + "BugReports": "https://github.com/jeroen/openssl/issues", + "SystemRequirements": "OpenSSL >= 1.0.2", + "VignetteBuilder": "knitr", + "Imports": [ + "askpass" + ], + "Suggests": [ + "curl", + "testthat (>= 2.1.0)", + "digest", + "knitr", + "rmarkdown", + "jsonlite", + "jose", + "sodium" + ], + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (ORCID: ), Oliver Keyes [ctb]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, + "parallelly": { + "Package": "parallelly", + "Version": "1.45.0", + "Source": "Repository", + "Title": "Enhancing the 'parallel' Package", + "Imports": [ + "parallel", + "tools", + "utils" + ], + "Suggests": [ + "commonmark", + "base64enc" + ], + "VignetteBuilder": "parallelly", + "Authors@R": "c( person(\"Henrik\", \"Bengtsson\", role = c(\"aut\", \"cre\", \"cph\"), email = \"henrikb@braju.com\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Mike\", \"Cheng\", role = c(\"ctb\"), email = \"mikefc@coolbutuseless.com\") )", + "Description": "Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.", + "License": "LGPL (>= 2.1)", + "LazyLoad": "TRUE", + "ByteCompile": "TRUE", + "URL": "https://parallelly.futureverse.org, https://github.com/futureverse/parallelly", + "BugReports": "https://github.com/futureverse/parallelly/issues", + "Language": "en-US", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Henrik Bengtsson [aut, cre, cph] (ORCID: ), Mike Cheng [ctb]", + "Maintainer": "Henrik Bengtsson ", + "Repository": "CRAN" + }, + "patchwork": { + "Package": "patchwork", + "Version": "1.3.1", + "Source": "Repository", + "Type": "Package", + "Title": "The Composer of Plots", + "Authors@R": "person(given = \"Thomas Lin\", family = \"Pedersen\", role = c(\"cre\", \"aut\"), email = \"thomasp85@gmail.com\", comment = c(ORCID = \"0000-0002-5147-4711\"))", + "Maintainer": "Thomas Lin Pedersen ", + "Description": "The 'ggplot2' package provides a strong API for sequentially building up a plot, but does not concern itself with composition of multiple plots. 'patchwork' is a package that expands the API to allow for arbitrarily complex composition of plots by, among others, providing mathematical operators for combining multiple plots. Other packages that try to address this need (but with a different approach) are 'gridExtra' and 'cowplot'.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Imports": [ + "ggplot2 (>= 3.0.0)", + "gtable (>= 0.3.6)", + "grid", + "stats", + "grDevices", + "utils", + "graphics", + "rlang (>= 1.0.0)", + "cli", + "farver" + ], + "RoxygenNote": "7.3.2", + "URL": "https://patchwork.data-imaginist.com, https://github.com/thomasp85/patchwork", + "BugReports": "https://github.com/thomasp85/patchwork/issues", + "Suggests": [ + "knitr", + "rmarkdown", + "gridGraphics", + "gridExtra", + "ragg", + "testthat (>= 2.1.0)", + "vdiffr", + "covr", + "png", + "gt (>= 0.11.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "gifski", + "NeedsCompilation": "no", + "Author": "Thomas Lin Pedersen [cre, aut] (ORCID: )", + "Repository": "CRAN" + }, + "pbapply": { + "Package": "pbapply", + "Version": "1.7-2", + "Source": "Repository", + "Type": "Package", + "Title": "Adding Progress Bar to '*apply' Functions", + "Date": "2023-06-27", + "Authors@R": "c(person(given = \"Peter\", family = \"Solymos\", comment = c(ORCID = \"0000-0001-7337-1740\"), role = c(\"aut\", \"cre\"), email = \"psolymos@gmail.com\"), person(given = \"Zygmunt\", family = \"Zawadzki\", role = \"aut\", email = \"zygmunt@zstat.pl\"), person(given = \"Henrik\", family = \"Bengtsson\", role = \"ctb\", email = \"henrikb@braju.com\"), person(\"R Core Team\", role = c(\"cph\", \"ctb\")))", + "Maintainer": "Peter Solymos ", + "Description": "A lightweight package that adds progress bar to vectorized R functions ('*apply'). The implementation can easily be added to functions where showing the progress is useful (e.g. bootstrap). The type and style of the progress bar (with percentages or remaining time) can be set through options. Supports several parallel processing backends including future.", + "Depends": [ + "R (>= 3.2.0)" + ], + "Imports": [ + "parallel" + ], + "Suggests": [ + "shiny", + "future", + "future.apply" + ], + "License": "GPL (>= 2)", + "URL": "https://github.com/psolymos/pbapply", + "BugReports": "https://github.com/psolymos/pbapply/issues", + "NeedsCompilation": "no", + "Author": "Peter Solymos [aut, cre] (), Zygmunt Zawadzki [aut], Henrik Bengtsson [ctb], R Core Team [cph, ctb]", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "pbkrtest": { + "Package": "pbkrtest", + "Version": "0.5.4", + "Source": "Repository", + "Title": "Parametric Bootstrap, Kenward-Roger and Satterthwaite Based Methods for Test in Mixed Models", + "Authors@R": "c( person(given = \"Ulrich\", family = \"Halekoh\", email = \"uhalekoh@health.sdu.dk\", role = c(\"aut\", \"cph\")), person(given = \"Søren\", family = \"Højsgaard\", email = \"sorenh@math.aau.dk\", role = c(\"aut\", \"cre\", \"cph\")) )", + "Maintainer": "Søren Højsgaard ", + "Description": "Computes p-values based on (a) Satterthwaite or Kenward-Rogers degree of freedom methods and (b) parametric bootstrap for mixed effects models as implemented in the 'lme4' package. Implements parametric bootstrap test for generalized linear mixed models as implemented in 'lme4' and generalized linear models. The package is documented in the paper by Halekoh and Højsgaard, (2012, ). 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It can check if a background process is running; wait on a background process to finish; get the exit status of finished processes; kill background processes. It can read the standard output and error of the processes, using non-blocking connections. 'processx' can poll a process for standard output or error, with a timeout. 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They work in terminals, in 'Emacs' 'ESS', 'RStudio', 'Windows' 'Rgui' and the 'macOS' 'R.app'. 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The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates, e.g. in the terminal using utils::txtProgressBar(), cli::cli_progress_bar(), in a graphical user interface using utils::winProgressBar(), tcltk::tkProgressBar() or shiny::withProgress(), via the speakers using beepr::beep(), or on a file system via the size of a file. Anyone can add additional, customized, progression handlers. The 'progressr' package uses R's condition framework for signaling progress updated. Because of this, progress can be reported from almost anywhere in R, e.g. from classical for and while loops, from map-reduce API:s like the lapply() family of functions, 'purrr', 'plyr', and 'foreach'. It will also work with parallel processing via the 'future' framework, e.g. future.apply::future_lapply(), furrr::future_map(), and 'foreach' with 'doFuture'. The package is compatible with Shiny applications.", + "Authors@R": "c(person(\"Henrik\", \"Bengtsson\", role = c(\"aut\", \"cre\", \"cph\"), email = \"henrikb@braju.com\", comment = c(ORCID = \"0000-0002-7579-5165\")))", + "License": "GPL (>= 3)", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "digest", + "utils" + ], + "Suggests": [ + "graphics", + "tcltk", + "beepr", + "cli", + "crayon", + "pbmcapply", + "progress", + "purrr", + "foreach", + "plyr", + "doFuture", + "future", + "future.apply", + "furrr", + "ntfy", + "RPushbullet", + "rstudioapi", + "shiny", + "commonmark", + "base64enc", + "tools" + ], + "VignetteBuilder": "progressr", + "URL": "https://progressr.futureverse.org, https://github.com/futureverse/progressr", + "BugReports": "https://github.com/futureverse/progressr/issues", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Henrik Bengtsson [aut, cre, cph] ()", + "Maintainer": "Henrik Bengtsson ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "promises": { + "Package": "promises", + "Version": "1.3.2", + "Source": "Repository", + "Type": "Package", + "Title": "Abstractions for Promise-Based Asynchronous Programming", + "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides fundamental abstractions for doing asynchronous programming in R using promises. Asynchronous programming is useful for allowing a single R process to orchestrate multiple tasks in the background while also attending to something else. Semantics are similar to 'JavaScript' promises, but with a syntax that is idiomatic R.", + "License": "MIT + file LICENSE", + "URL": "https://rstudio.github.io/promises/, https://github.com/rstudio/promises", + "BugReports": "https://github.com/rstudio/promises/issues", + "Imports": [ + "fastmap (>= 1.1.0)", + "later", + "magrittr (>= 1.5)", + "R6", + "Rcpp", + "rlang", + "stats" + ], + "Suggests": [ + "future (>= 1.21.0)", + "knitr", + "purrr", + "rmarkdown", + "spelling", + "testthat", + "vembedr" + ], + "LinkingTo": [ + "later", + "Rcpp" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "rsconnect", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Joe Cheng [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Joe Cheng ", + "Repository": "CRAN" + }, + "ps": { + "Package": "ps", + "Version": "1.9.1", + "Source": "Repository", + "Title": "List, Query, Manipulate System Processes", + "Authors@R": "c( person(\"Jay\", \"Loden\", role = \"aut\"), person(\"Dave\", \"Daeschler\", role = \"aut\"), person(\"Giampaolo\", \"Rodola'\", role = \"aut\"), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "List, query and manipulate all system processes, on 'Windows', 'Linux' and 'macOS'.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/r-lib/ps, https://ps.r-lib.org/", + "BugReports": "https://github.com/r-lib/ps/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "utils" + ], + "Suggests": [ + "callr", + "covr", + "curl", + "pillar", + "pingr", + "processx (>= 3.1.0)", + "R6", + "rlang", + "testthat (>= 3.0.0)", + "webfakes", + "withr" + ], + "Biarch": "true", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Jay Loden [aut], Dave Daeschler [aut], Giampaolo Rodola' [aut], Gábor Csárdi [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, + "psych": { + "Package": "psych", + "Version": "2.5.6", + "Source": "Repository", + "Date": "2025-06-20", + "Title": "Procedures for Psychological, Psychometric, and Personality Research", + "Authors@R": "person(\"William\", \"Revelle\", role =c(\"aut\",\"cre\"), email=\"revelle@northwestern.edu\", comment=c(ORCID = \"0000-0003-4880-9610\") )", + "Description": "A general purpose toolbox developed originally for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Validation and cross validation of scales developed using basic machine learning algorithms are provided, as are functions for simulating and testing particular item and test structures. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, including mediation models, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometric theory as well as publications in personality research. For more information, see the web page.", + "License": "GPL (>= 2)", + "Imports": [ + "mnormt", + "parallel", + "stats", + "graphics", + "grDevices", + "methods", + "lattice", + "nlme", + "GPArotation" + ], + "Suggests": [ + "psychTools", + "lavaan", + "lme4", + "Rcsdp", + "graph", + "knitr", + "Rgraphviz" + ], + "LazyData": "yes", + "ByteCompile": "true", + "VignetteBuilder": "knitr", + "URL": "https://personality-project.org/r/psych/ https://personality-project.org/r/psych-manual.pdf", + "NeedsCompilation": "no", + "Author": "William Revelle [aut, cre] (ORCID: )", + "Maintainer": "William Revelle ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "purrr": { + "Package": "purrr", + "Version": "1.1.0", + "Source": "Repository", + "Title": "Functional Programming Tools", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"https://ror.org/03wc8by49\")) )", + "Description": "A complete and consistent functional programming toolkit for R.", + "License": "MIT + file LICENSE", + "URL": "https://purrr.tidyverse.org/, https://github.com/tidyverse/purrr", + "BugReports": "https://github.com/tidyverse/purrr/issues", + "Depends": [ + "R (>= 4.1)" + ], + "Imports": [ + "cli (>= 3.6.1)", + "lifecycle (>= 1.0.3)", + "magrittr (>= 1.5.0)", + "rlang (>= 1.1.1)", + "vctrs (>= 0.6.3)" + ], + "Suggests": [ + "carrier (>= 0.2.0)", + "covr", + "dplyr (>= 0.7.8)", + "httr", + "knitr", + "lubridate", + "mirai (>= 2.4.0)", + "rmarkdown", + "testthat (>= 3.0.0)", + "tibble", + "tidyselect" + ], + "LinkingTo": [ + "cli" + ], + "VignetteBuilder": "knitr", + "Biarch": "true", + "Config/build/compilation-database": "true", + "Config/Needs/website": "tidyverse/tidytemplate, tidyr", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "TRUE", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre] (ORCID: ), Lionel Henry [aut], Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "quantreg": { + "Package": "quantreg", + "Version": "6.1", + "Source": "Repository", + "Title": "Quantile Regression", + "Description": "Estimation and inference methods for models for conditional quantile functions: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also now included. See Koenker, R. (2005) Quantile Regression, Cambridge U. Press, and Koenker, R. et al. (2017) Handbook of Quantile Regression, CRC Press, .", + "Authors@R": "c( person(\"Roger\", \"Koenker\", role = c(\"cre\",\"aut\"), email = \"rkoenker@illinois.edu\"), person(\"Stephen\", \"Portnoy\", role = c(\"ctb\"), comment = \"Contributions to Censored QR code\", email = \"sportnoy@illinois.edu\"), person(c(\"Pin\", \"Tian\"), \"Ng\", role = c(\"ctb\"), comment = \"Contributions to Sparse QR code\", email = \"pin.ng@nau.edu\"), person(\"Blaise\", \"Melly\", role = c(\"ctb\"), comment = \"Contributions to preprocessing code\", email = \"mellyblaise@gmail.com\"), person(\"Achim\", \"Zeileis\", role = c(\"ctb\"), comment = \"Contributions to dynrq code essentially identical to his dynlm code\", email = \"Achim.Zeileis@uibk.ac.at\"), person(\"Philip\", \"Grosjean\", role = c(\"ctb\"), comment = \"Contributions to nlrq code\", email = \"phgrosjean@sciviews.org\"), person(\"Cleve\", \"Moler\", role = c(\"ctb\"), comment = \"author of several linpack routines\"), person(\"Yousef\", \"Saad\", role = c(\"ctb\"), comment = \"author of sparskit2\"), person(\"Victor\", \"Chernozhukov\", role = c(\"ctb\"), comment = \"contributions to extreme value inference code\"), person(\"Ivan\", \"Fernandez-Val\", role = c(\"ctb\"), comment = \"contributions to extreme value inference code\"), person(\"Martin\", \"Maechler\", role = \"ctb\", comment = c(\"tweaks (src/chlfct.f, 'tiny','Large')\", ORCID = \"0000-0002-8685-9910\")), person(c(\"Brian\", \"D\"), \"Ripley\", role = c(\"trl\",\"ctb\"), comment = \"Initial (2001) R port from S (to my everlasting shame -- how could I have been so slow to adopt R!) and for numerous other suggestions and useful advice\", email = \"ripley@stats.ox.ac.uk\"))", + "Maintainer": "Roger Koenker ", + "Repository": "CRAN", + "Depends": [ + "R (>= 3.5)", + "stats", + "SparseM" + ], + "Imports": [ + "methods", + "graphics", + "Matrix", + "MatrixModels", + "survival", + "MASS" + ], + "Suggests": [ + "interp", + "rgl", + "logspline", + "nor1mix", + "Formula", + "zoo", + "R.rsp", + "conquer" + ], + "License": "GPL (>= 2)", + "URL": "https://www.r-project.org", + "NeedsCompilation": "yes", + "VignetteBuilder": "R.rsp", + "Author": "Roger Koenker [cre, aut], Stephen Portnoy [ctb] (Contributions to Censored QR code), Pin Tian Ng [ctb] (Contributions to Sparse QR code), Blaise Melly [ctb] (Contributions to preprocessing code), Achim Zeileis [ctb] (Contributions to dynrq code essentially identical to his dynlm code), Philip Grosjean [ctb] (Contributions to nlrq code), Cleve Moler [ctb] (author of several linpack routines), Yousef Saad [ctb] (author of sparskit2), Victor Chernozhukov [ctb] (contributions to extreme value inference code), Ivan Fernandez-Val [ctb] (contributions to extreme value inference code), Martin Maechler [ctb] (tweaks (src/chlfct.f, 'tiny','Large'), ), Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my everlasting shame -- how could I have been so slow to adopt R!) and for numerous other suggestions and useful advice)" + }, + "ragg": { + "Package": "ragg", + "Version": "1.4.0", + "Source": "Repository", + "Type": "Package", + "Title": "Graphic Devices Based on AGG", + "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Maxim\", \"Shemanarev\", role = c(\"aut\", \"cph\"), comment = \"Author of AGG\"), person(\"Tony\", \"Juricic\", , \"tonygeek@yahoo.com\", role = c(\"ctb\", \"cph\"), comment = \"Contributor to AGG\"), person(\"Milan\", \"Marusinec\", , \"milan@marusinec.sk\", role = c(\"ctb\", \"cph\"), comment = \"Contributor to AGG\"), person(\"Spencer\", \"Garrett\", role = \"ctb\", comment = \"Contributor to AGG\"), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Maintainer": "Thomas Lin Pedersen ", + "Description": "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D drawing library. The 'ragg' package provides a set of graphic devices based on AGG to use as alternative to the raster devices provided through the 'grDevices' package.", + "License": "MIT + file LICENSE", + "URL": "https://ragg.r-lib.org, https://github.com/r-lib/ragg", + "BugReports": "https://github.com/r-lib/ragg/issues", + "Imports": [ + "systemfonts (>= 1.0.3)", + "textshaping (>= 0.3.0)" + ], + "Suggests": [ + "covr", + "graphics", + "grid", + "testthat (>= 3.0.0)" + ], + "LinkingTo": [ + "systemfonts", + "textshaping" + ], + "Config/Needs/website": "ggplot2, devoid, magick, bench, tidyr, ggridges, hexbin, sessioninfo, pkgdown, tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "SystemRequirements": "freetype2, libpng, libtiff, libjpeg", + "Config/testthat/edition": "3", + "Config/build/compilation-database": "true", + "NeedsCompilation": "yes", + "Author": "Thomas Lin Pedersen [cre, aut] (), Maxim Shemanarev [aut, cph] (Author of AGG), Tony Juricic [ctb, cph] (Contributor to AGG), Milan Marusinec [ctb, cph] (Contributor to AGG), Spencer Garrett [ctb] (Contributor to AGG), Posit, PBC [cph, fnd]", + "Repository": "CRAN" + }, + "rappdirs": { + "Package": "rappdirs", + "Version": "0.3.3", + "Source": "Repository", + "Type": "Package", + "Title": "Application Directories: Determine Where to Save Data, Caches, and Logs", + "Authors@R": "c(person(given = \"Hadley\", family = \"Wickham\", role = c(\"trl\", \"cre\", \"cph\"), email = \"hadley@rstudio.com\"), person(given = \"RStudio\", role = \"cph\"), person(given = \"Sridhar\", family = \"Ratnakumar\", role = \"aut\"), person(given = \"Trent\", family = \"Mick\", role = \"aut\"), person(given = \"ActiveState\", role = \"cph\", comment = \"R/appdir.r, R/cache.r, R/data.r, R/log.r translated from appdirs\"), person(given = \"Eddy\", family = \"Petrisor\", role = \"ctb\"), person(given = \"Trevor\", family = \"Davis\", role = c(\"trl\", \"aut\")), person(given = \"Gabor\", family = \"Csardi\", role = \"ctb\"), person(given = \"Gregory\", family = \"Jefferis\", role = \"ctb\"))", + "Description": "An easy way to determine which directories on the users computer you should use to save data, caches and logs. A port of Python's 'Appdirs' () to R.", + "License": "MIT + file LICENSE", + "URL": "https://rappdirs.r-lib.org, https://github.com/r-lib/rappdirs", + "BugReports": "https://github.com/r-lib/rappdirs/issues", + "Depends": [ + "R (>= 3.2)" + ], + "Suggests": [ + "roxygen2", + "testthat (>= 3.0.0)", + "covr", + "withr" + ], + "Copyright": "Original python appdirs module copyright (c) 2010 ActiveState Software Inc. R port copyright Hadley Wickham, RStudio. See file LICENSE for details.", + "Encoding": "UTF-8", + "RoxygenNote": "7.1.1", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [trl, cre, cph], RStudio [cph], Sridhar Ratnakumar [aut], Trent Mick [aut], ActiveState [cph] (R/appdir.r, R/cache.r, R/data.r, R/log.r translated from appdirs), Eddy Petrisor [ctb], Trevor Davis [trl, aut], Gabor Csardi [ctb], Gregory Jefferis [ctb]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "rbibutils": { + "Package": "rbibutils", + "Version": "2.3", + "Source": "Repository", + "Type": "Package", + "Title": "Read 'Bibtex' Files and Convert Between Bibliography Formats", + "Authors@R": "c( person(given = c(\"Georgi\", \"N.\"), family = \"Boshnakov\", role = c(\"aut\", \"cre\"), \t email = \"georgi.boshnakov@manchester.ac.uk\", comment = \"R port, R code, new C code and modifications to bibutils' C code, conversion to Bibentry (R and C code)\" ), person(given = \"Chris\", family = \"Putman\", role = \"aut\", comment = \"src/*, author of the bibutils libraries, https://sourceforge.net/projects/bibutils/\"), person(given = \"Richard\", family = \"Mathar\", role = \"ctb\", comment = \"src/addsout.c\"), person(given = \"Johannes\", family = \"Wilm\", role = \"ctb\", comment = \"src/biblatexin.c, src/bltypes.c\"), person(\"R Core Team\", role = \"ctb\", comment = \"base R's bibentry and bibstyle implementation\") )", + "Description": "Read and write 'Bibtex' files. Convert between bibliography formats, including 'Bibtex', 'Biblatex', 'PubMed', 'Endnote', and 'Bibentry'. Includes a port of the 'bibutils' utilities by Chris Putnam . Supports all bibliography formats and character encodings implemented in 'bibutils'.", + "License": "GPL-2", + "URL": "https://geobosh.github.io/rbibutils/ (doc), https://github.com/GeoBosh/rbibutils (devel)", + "BugReports": "https://github.com/GeoBosh/rbibutils/issues", + "Depends": [ + "R (>= 2.10)" + ], + "Imports": [ + "utils", + "tools" + ], + "Suggests": [ + "testthat" + ], + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Config/Needs/memcheck": "devtools, rcmdcheck", + "Author": "Georgi N. Boshnakov [aut, cre] (R port, R code, new C code and modifications to bibutils' C code, conversion to Bibentry (R and C code)), Chris Putman [aut] (src/*, author of the bibutils libraries, https://sourceforge.net/projects/bibutils/), Richard Mathar [ctb] (src/addsout.c), Johannes Wilm [ctb] (src/biblatexin.c, src/bltypes.c), R Core Team [ctb] (base R's bibentry and bibstyle implementation)", + "Maintainer": "Georgi N. Boshnakov ", + "Repository": "CRAN" + }, + "readr": { + "Package": "readr", + "Version": "2.1.5", + "Source": "Repository", + "Title": "Read Rectangular Text Data", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Romain\", \"Francois\", role = \"ctb\"), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Shelby\", \"Bearrows\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"https://github.com/mandreyel/\", role = \"cph\", comment = \"mio library\"), person(\"Jukka\", \"Jylänki\", role = c(\"ctb\", \"cph\"), comment = \"grisu3 implementation\"), person(\"Mikkel\", \"Jørgensen\", role = c(\"ctb\", \"cph\"), comment = \"grisu3 implementation\") )", + "Description": "The goal of 'readr' is to provide a fast and friendly way to read rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.", + "License": "MIT + file LICENSE", + "URL": "https://readr.tidyverse.org, https://github.com/tidyverse/readr", + "BugReports": "https://github.com/tidyverse/readr/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cli (>= 3.2.0)", + "clipr", + "crayon", + "hms (>= 0.4.1)", + "lifecycle (>= 0.2.0)", + "methods", + "R6", + "rlang", + "tibble", + "utils", + "vroom (>= 1.6.0)" + ], + "Suggests": [ + "covr", + "curl", + "datasets", + "knitr", + "rmarkdown", + "spelling", + "stringi", + "testthat (>= 3.2.0)", + "tzdb (>= 0.1.1)", + "waldo", + "withr", + "xml2" + ], + "LinkingTo": [ + "cpp11", + "tzdb (>= 0.1.1)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "false", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut], Jim Hester [aut], Romain Francois [ctb], Jennifer Bryan [aut, cre] (), Shelby Bearrows [ctb], Posit Software, PBC [cph, fnd], https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [ctb, cph] (grisu3 implementation), Mikkel Jørgensen [ctb, cph] (grisu3 implementation)", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" + }, + "readxl": { + "Package": "readxl", + "Version": "1.4.5", + "Source": "Repository", + "Title": "Read Excel Files", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\"), comment = \"Copyright holder of all R code and all C/C++ code without explicit copyright attribution\"), person(\"Marcin\", \"Kalicinski\", role = c(\"ctb\", \"cph\"), comment = \"Author of included RapidXML code\"), person(\"Komarov Valery\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Christophe Leitienne\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Bob Colbert\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"David Hoerl\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Evan Miller\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\") )", + "Description": "Import excel files into R. Supports '.xls' via the embedded 'libxls' C library and '.xlsx' via the embedded 'RapidXML' C++ library . 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\"Sainsbury\", role=\"ctb\"), person(\"Dietrich\", \"Stoyan\", role=\"ctb\"), person(\"David\", \"Strauss\", role=\"ctb\"), person(\"L\", \"Strand\", role=\"ctb\"), person(\"Masaharu\", \"Tanemura\", role=\"ctb\"), person(\"Graham\", \"Upton\", role=\"ctb\"), person(\"Bill\", \"Venables\", role=\"ctb\"), person(\"Ulrich\", \"Vogel\", role=\"ctb\"), person(\"Sasha\", \"Voss\", role=\"ctb\"), person(\"Rasmus\", \"Waagepetersen\", role=\"ctb\"), person(\"Keith\", \"Watkins\", role=\"ctb\"), person(\"H\", \"Wendrock\", role=\"ctb\") )", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "spatstat.utils (>= 3.1-2)", + "Matrix" + ], + "Suggests": [ + "spatstat.geom", + "spatstat.random", + "spatstat.explore", + "spatstat.model", + "spatstat.linnet" + ], + "Description": "Contains all the datasets for the 'spatstat' family of packages.", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "LazyData": "true", + "NeedsCompilation": "no", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.data/issues", + "Author": "Adrian Baddeley [aut, cre] (), Rolf Turner [aut] (), Ege Rubak [aut] (), W Aherne [ctb], Freda Alexander [ctb], Qi Wei Ang [ctb], Sourav Banerjee [ctb], Mark Berman [ctb], R Bernhardt [ctb], Thomas Berndtsen [ctb], Andrew Bevan [ctb], Jeffrey Betts [ctb], Ray Cartwright [ctb], Lucia Cobo Sanchez [ctb], Richard Condit [ctb], Francis Crick [ctb], Marcelino de la Cruz Rot [ctb], Jack Cuzick [ctb], Tilman Davies [ctb], Peter Diggle [ctb], Michael Drinkwater [ctb], Stephen Eglen [ctb], Robert Edwards [ctb], Johannes Elias [ctb], AE Esler [ctb], Gregory Evans [ctb], Bernard Fingleton [ctb], Olivier Flores [ctb], David Ford [ctb], Robin Foster [ctb], Janet Franklin [ctb], Neba Funwi-Gabga [ctb], DJ Gerrard [ctb], Andy Green [ctb], Tim Griffin [ctb], Ute Hahn [ctb], RD Harkness [ctb], Arthur Hickman [ctb], Stephen Hubbell [ctb], Austin Hughes [ctb], Jonathan Huntington [ctb], MJ Hutchings [ctb], Jackie Inwald [ctb], Valerie Isham [ctb], Aruna Jammalamadaka [ctb], Carl Knox-Robinson [ctb], Mahdieh Khanmohammadi [ctb], Tero Kokkila [ctb], Bas Kooijman [ctb], Kenneth Kosik [ctb], Peter Kovesi [ctb], Lily Kozmian-Ledward [ctb], Robert Lamb [ctb], NA Laskurain [ctb], George Leser [ctb], Marie-Colette van Lieshout [ctb], AF Mark [ctb], Sebastian Meyer [ctb], Jorge Mateu [ctb], Annikki Makela [ctb], Enrique Miranda [ctb], Nicoletta Nava [ctb], M Numata [ctb], Matti Nummelin [ctb], Jens Randel Nyengaard [ctb], Yosihiko Ogata [ctb], Si Palmer [ctb], Antti Penttinen [ctb], Sandra Pereira [ctb], Nicolas Picard [ctb], William Platt [ctb], Stephen Rathbun [ctb], Brian Ripley [ctb], Roger Sainsbury [ctb], Dietrich Stoyan [ctb], David Strauss [ctb], L Strand [ctb], Masaharu Tanemura [ctb], Graham Upton [ctb], Bill Venables [ctb], Ulrich Vogel [ctb], Sasha Voss [ctb], Rasmus Waagepetersen [ctb], Keith Watkins [ctb], H Wendrock [ctb]", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "spatstat.explore": { + "Package": "spatstat.explore", + "Version": "3.4-3", + "Source": "Repository", + "Date": "2025-05-21", + "Title": "Exploratory Data Analysis for the 'spatstat' Family", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Kasper\", \"Klitgaard Berthelsen\", role = \"ctb\"), person(\"Warick\", \"Brown\", role = \"cph\"), person(\"Achmad\", \"Choiruddin\", role = \"ctb\"), person(\"Ya-Mei\", \"Chang\", role = \"ctb\"), person(\"Jean-Francois\", \"Coeurjolly\", role = \"ctb\"), person(\"Ottmar\", \"Cronie\", role = \"ctb\"), person(\"Tilman\", \"Davies\", role = c(\"ctb\", \"cph\")), person(\"Julian\", \"Gilbey\", role = \"ctb\"), person(\"Jonatan\", \"Gonzalez\", role = \"ctb\"), person(\"Yongtao\", \"Guan\", role = \"ctb\"), person(\"Ute\", \"Hahn\", role = \"ctb\"), person(\"Martin\", \"Hazelton\", role = \"ctb\"), person(\"Kassel\", \"Hingee\", role = c(\"ctb\", \"cph\")), person(\"Abdollah\", \"Jalilian\", role = \"ctb\"), person(\"Frederic\", \"Lavancier\", role = \"ctb\"), person(\"Marie-Colette\", \"van Lieshout\", role = c(\"ctb\", \"cph\")), person(\"Greg\", \"McSwiggan\", role = \"ctb\"), person(\"Robin K\", \"Milne\", role = \"cph\"), person(\"Tuomas\", \"Rajala\", role = \"ctb\"), person(\"Suman\", \"Rakshit\", role = c(\"ctb\", \"cph\")), person(\"Dominic\", \"Schuhmacher\", role = \"ctb\"), person(\"Rasmus\", \"Plenge Waagepetersen\", role = \"ctb\"), person(\"Hangsheng\", \"Wang\", role = \"ctb\"), person(\"Tingting\", \"Zhan\", role=\"ctb\"))", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)", + "spatstat.data (>= 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(Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "NeedsCompilation": "yes", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.explore/issues", + "Author": "Adrian Baddeley [aut, cre, cph] (ORCID: ), Rolf Turner [aut, cph] (ORCID: ), Ege Rubak [aut, cph] (ORCID: ), Kasper Klitgaard Berthelsen [ctb], Warick Brown [cph], Achmad Choiruddin [ctb], Ya-Mei Chang [ctb], Jean-Francois Coeurjolly [ctb], Ottmar Cronie [ctb], Tilman Davies [ctb, cph], Julian Gilbey [ctb], Jonatan Gonzalez [ctb], Yongtao Guan [ctb], Ute Hahn [ctb], Martin Hazelton [ctb], Kassel Hingee [ctb, cph], Abdollah Jalilian [ctb], Frederic Lavancier [ctb], Marie-Colette van Lieshout [ctb, cph], Greg McSwiggan [ctb], Robin K Milne [cph], Tuomas Rajala [ctb], Suman Rakshit [ctb, cph], Dominic Schuhmacher [ctb], Rasmus Plenge Waagepetersen [ctb], Hangsheng Wang [ctb], Tingting Zhan [ctb]", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "spatstat.geom": { + "Package": "spatstat.geom", + "Version": "3.4-1", + "Source": "Repository", + "Date": "2025-05-20", + "Title": "Geometrical Functionality of the 'spatstat' Family", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Warick\", \"Brown\" , role = \"ctb\"), person(\"Tilman\", \"Davies\", role = \"ctb\"), person(\"Ute\", \"Hahn\", role = \"ctb\"), person(\"Martin\", \"Hazelton\", role = \"ctb\"), person(\"Abdollah\", \"Jalilian\", role = \"ctb\"), person(\"Greg\", \"McSwiggan\", role = c(\"ctb\", \"cph\")), person(\"Sebastian\", \"Meyer\", role = c(\"ctb\", \"cph\")), person(\"Jens\", \"Oehlschlaegel\", role = c(\"ctb\", \"cph\")), person(\"Suman\", \"Rakshit\", role = \"ctb\"), person(\"Dominic\", \"Schuhmacher\", role = \"ctb\"), person(\"Rasmus\", \"Waagepetersen\", role = \"ctb\"))", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)", + "spatstat.data (>= 3.1)", + "spatstat.univar (>= 3.1)", + "stats", + "graphics", + "grDevices", + "utils", + "methods" + ], + "Imports": [ + "spatstat.utils (>= 3.1-4)", + "deldir (>= 1.0-2)", + "polyclip (>= 1.10)" + ], + "Suggests": [ + "spatstat.random (>= 3.3)", + "spatstat.explore (>= 3.3)", + "spatstat.model (>= 3.3)", + "spatstat.linnet (>= 3.2)", + "spatial", + "fftwtools (>= 0.9-8)", + "spatstat (>= 3.3)" + ], + "Description": "Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), pixel images, line segment patterns, tessellations and hyperframes. Capabilities include creation and manipulation of data (using command line or graphical interaction), plotting, geometrical operations (rotation, shift, rescale, affine transformation), convex hull, discretisation and pixellation, Dirichlet tessellation, Delaunay triangulation, pairwise distances, nearest-neighbour distances, distance transform, morphological operations (erosion, dilation, closing, opening), quadrat counting, geometrical measurement, geometrical covariance, colour maps, calculus on spatial domains, Gaussian blur, level sets of images, transects of images, intersections between objects, minimum distance matching. (Excludes spatial data on a network, which are supported by the package 'spatstat.linnet'.)", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "NeedsCompilation": "yes", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.geom/issues", + "Author": "Adrian Baddeley [aut, cre, cph] (ORCID: ), Rolf Turner [aut, cph] (ORCID: ), Ege Rubak [aut, cph] (ORCID: ), Warick Brown [ctb], Tilman Davies [ctb], Ute Hahn [ctb], Martin Hazelton [ctb], Abdollah Jalilian [ctb], Greg McSwiggan [ctb, cph], Sebastian Meyer [ctb, cph], Jens Oehlschlaegel [ctb, cph], Suman Rakshit [ctb], Dominic Schuhmacher [ctb], Rasmus Waagepetersen [ctb]", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "spatstat.random": { + "Package": "spatstat.random", + "Version": "3.4-1", + "Source": "Repository", + "Date": "2025-05-20", + "Title": "Random Generation Functionality for the 'spatstat' Family", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Tilman\", \"Davies\", role = c(\"aut\", \"cph\"), comment=c(ORCID=\"0000-0003-0565-1825\")), person(\"Kasper\", \"Klitgaard Berthelsen\", role = c(\"ctb\", \"cph\")), person(\"David\", \"Bryant\", role = c(\"ctb\", \"cph\")), person(\"Ya-Mei\", \"Chang\", role = c(\"ctb\", \"cph\"), email = \"yamei628@gmail.com\"), person(\"Ute\", \"Hahn\", role = \"ctb\"), person(\"Abdollah\", \"Jalilian\", role = \"ctb\"), person(\"Dominic\", \"Schuhmacher\", role = c(\"ctb\", \"cph\")), person(\"Rasmus\", \"Plenge Waagepetersen\", role = c(\"ctb\", \"cph\")))", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)", + "spatstat.data (>= 3.1)", + "spatstat.univar (>= 3.1)", + "spatstat.geom (>= 3.3-6)", + "stats", + "utils", + "methods", + "grDevices" + ], + "Imports": [ + "spatstat.utils (>= 3.1-4)" + ], + "Suggests": [ + "spatial", + "spatstat.linnet (>= 3.2)", + "spatstat.explore", + "spatstat.model", + "spatstat (>= 3.3)", + "gsl" + ], + "Description": "Functionality for random generation of spatial data in the 'spatstat' family of packages. Generates random spatial patterns of points according to many simple rules (complete spatial randomness, Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns (thinning, random shift, jittering), simulated realisations of random point processes including simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes (using direct, Brix-Kendall, or hybrid algorithms), log-Gaussian Cox processes, product shot noise cluster processes and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs sampler, or coupling-from-the-past perfect simulation). Also generates random spatial patterns of line segments, random tessellations, and random images (random noise, random mosaics). Excludes random generation on a linear network, which is covered by the separate package 'spatstat.linnet'.", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "NeedsCompilation": "yes", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.random/issues", + "Author": "Adrian Baddeley [aut, cre, cph] (ORCID: ), Rolf Turner [aut, cph] (ORCID: ), Ege Rubak [aut, cph] (ORCID: ), Tilman Davies [aut, cph] (ORCID: ), Kasper Klitgaard Berthelsen [ctb, cph], David Bryant [ctb, cph], Ya-Mei Chang [ctb, cph], Ute Hahn [ctb], Abdollah Jalilian [ctb], Dominic Schuhmacher [ctb, cph], Rasmus Plenge Waagepetersen [ctb, cph]", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "spatstat.sparse": { + "Package": "spatstat.sparse", + "Version": "3.1-0", + "Source": "Repository", + "Date": "2024-06-21", + "Title": "Sparse Three-Dimensional Arrays and Linear Algebra Utilities", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")))", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)", + "stats", + "utils", + "methods", + "Matrix", + "abind", + "tensor" + ], + "Imports": [ + "spatstat.utils (>= 3.0-5)" + ], + "Description": "Defines sparse three-dimensional arrays and supports standard operations on them. The package also includes utility functions for matrix calculations that are common in statistics, such as quadratic forms.", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "NeedsCompilation": "yes", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.sparse/issues", + "Author": "Adrian Baddeley [aut, cre, cph] (), Rolf Turner [aut, cph] (), Ege Rubak [aut, cph] ()", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "spatstat.univar": { + "Package": "spatstat.univar", + "Version": "3.1-4", + "Source": "Repository", + "Date": "2025-07-13", + "Title": "One-Dimensional Probability Distribution Support for the 'spatstat' Family", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(c(\"Tilman\", \"M.\"), \"Davies\", role = c(\"aut\", \"ctb\", \"cph\"), email = \"Tilman.Davies@otago.ac.nz\", comment = c(ORCID=\"0000-0003-0565-1825\")), person(c(\"Martin\", \"L.\"), \"Hazelton\", role = c(\"aut\", \"ctb\", \"cph\"), email = \"Martin.Hazelton@otago.ac.nz\", comment = c(ORCID=\"0000-0001-7831-725X\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Greg\", \"McSwiggan\", role = c(\"ctb\", \"cph\")))", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)", + "stats" + ], + "Imports": [ + "spatstat.utils (>= 3.1-2)", + "graphics" + ], + "Description": "Estimation of one-dimensional probability distributions including kernel density estimation, weighted empirical cumulative distribution functions, Kaplan-Meier and reduced-sample estimators for right-censored data, heat kernels, kernel properties, quantiles and integration.", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "NeedsCompilation": "yes", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.univar/issues", + "Author": "Adrian Baddeley [aut, cre, cph] (ORCID: ), Tilman M. Davies [aut, ctb, cph] (ORCID: ), Martin L. Hazelton [aut, ctb, cph] (ORCID: ), Ege Rubak [aut, cph] (ORCID: ), Rolf Turner [aut, cph] (ORCID: ), Greg McSwiggan [ctb, cph]", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "spatstat.utils": { + "Package": "spatstat.utils", + "Version": "3.1-4", + "Source": "Repository", + "Date": "2025-05-15", + "Title": "Utility Functions for 'spatstat'", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = \"aut\", email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = \"aut\", email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")))", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)", + "stats", + "graphics", + "grDevices", + "utils", + "methods" + ], + "Suggests": [ + "spatstat.model" + ], + "Description": "Contains utility functions for the 'spatstat' family of packages which may also be useful for other purposes.", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "NeedsCompilation": "yes", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.utils/issues", + "Author": "Adrian Baddeley [aut, cre] (ORCID: ), Rolf Turner [aut] (ORCID: ), Ege Rubak [aut] (ORCID: )", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "speckle": { + "Package": "speckle", + "Version": "1.8.0", + "Source": "Bioconductor", + "Type": "Package", + "Title": "Statistical methods for analysing single cell RNA-seq data", + "Date": "2020-12-02", + "Authors@R": "c(person(given = \"Belinda\", family = \"Phipson\", role = c(\"aut\", \"cre\"), email = \"phipson.b@wehi.edu.au\") )", + "LazyData": "FALSE", + "Depends": [ + "R (>= 4.2.0)" + ], + "Imports": [ + "limma", + "edgeR", + "SingleCellExperiment", + "Seurat", + "ggplot2", + "methods", + "stats", + "grDevices", + "graphics" + ], + "VignetteBuilder": "knitr", + "Suggests": [ + "BiocStyle", + "knitr", + "rmarkdown", + "statmod", + "CellBench", + "scater", + "patchwork", + "jsonlite", + "vdiffr", + "testthat (>= 3.0.0)" + ], + "Description": "The speckle package contains functions for the analysis of single cell RNA-seq data. The speckle package currently contains functions to analyse differences in cell type proportions. There are also functions to estimate the parameters of the Beta distribution based on a given counts matrix, and a function to normalise a counts matrix to the median library size. There are plotting functions to visualise cell type proportions and the mean-variance relationship in cell type proportions and counts. As our research into specialised analyses of single cell data continues we anticipate that the package will be updated with new functions.", + "License": "GPL-3", + "biocViews": "SingleCell, RNASeq, Regression, GeneExpression", + "RoxygenNote": "7.2.2", + "Encoding": "UTF-8", + "Config/testthat/edition": "3", + "git_url": "https://git.bioconductor.org/packages/speckle", + "git_branch": "RELEASE_3_21", + "git_last_commit": "8b8d884", + "git_last_commit_date": "2025-04-15", + "Repository": "Bioconductor 3.21", + "NeedsCompilation": "no", + "Author": "Belinda Phipson [aut, cre]", + "Maintainer": "Belinda Phipson " + }, + "statmod": { + "Package": "statmod", + "Version": "1.5.0", + "Source": "Repository", + "Date": "2022-12-28", + "Title": "Statistical Modeling", + "Author": "Gordon Smyth [cre, aut], Lizhong Chen [aut], Yifang Hu [ctb], Peter Dunn [ctb], Belinda Phipson [ctb], Yunshun Chen [ctb]", + "Maintainer": "Gordon Smyth ", + "Depends": [ + "R (>= 3.0.0)" + ], + "Imports": [ + "stats", + "graphics" + ], + "Suggests": [ + "MASS", + "tweedie" + ], + "Description": "A collection of algorithms and functions to aid statistical modeling. 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This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.", + "Imports": [ + "xfun (>= 0.48)" + ], + "Suggests": [ + "testit", + "rstudioapi" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/rstudio/tinytex", + "BugReports": "https://github.com/rstudio/tinytex/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre, cph] (), Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] (), Devon Ryan [ctb] (), Ethan Heinzen [ctb], Fernando Cagua [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" + }, + "tzdb": { + "Package": "tzdb", + "Version": "0.5.0", + "Source": "Repository", + "Title": "Time Zone Database Information", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"Howard\", \"Hinnant\", role = \"cph\", comment = \"Author of the included date library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides an up-to-date copy of the Internet Assigned Numbers Authority (IANA) Time Zone Database. It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight saving time rules. Additionally, this package provides a C++ interface for working with the 'date' library. 'date' provides comprehensive support for working with dates and date-times, which this package exposes to make it easier for other R packages to utilize. Headers are provided for calendar specific calculations, along with a limited interface for time zone manipulations.", + "License": "MIT + file LICENSE", + "URL": "https://tzdb.r-lib.org, https://github.com/r-lib/tzdb", + "BugReports": "https://github.com/r-lib/tzdb/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "LinkingTo": [ + "cpp11 (>= 0.5.2)" + ], + "Biarch": "yes", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Davis Vaughan [aut, cre], Howard Hinnant [cph] (Author of the included date library), Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "utf8": { + "Package": "utf8", + "Version": "1.2.6", + "Source": "Repository", + "Title": "Unicode Text Processing", + "Authors@R": "c(person(given = c(\"Patrick\", \"O.\"), family = \"Perry\", role = c(\"aut\", \"cph\")), person(given = \"Kirill\", family = \"M\\u00fcller\", role = \"cre\", email = \"kirill@cynkra.com\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(given = \"Unicode, Inc.\", role = c(\"cph\", \"dtc\"), comment = \"Unicode Character Database\"))", + "Description": "Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.", + "License": "Apache License (== 2.0) | file LICENSE", + "URL": "https://krlmlr.github.io/utf8/, https://github.com/krlmlr/utf8", + "BugReports": "https://github.com/krlmlr/utf8/issues", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "cli", + "covr", + "knitr", + "rlang", + "rmarkdown", + "testthat (>= 3.0.0)", + "withr" + ], + "VignetteBuilder": "knitr, rmarkdown", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2.9000", + "NeedsCompilation": "yes", + "Author": "Patrick O. Perry [aut, cph], Kirill Müller [cre] (ORCID: ), Unicode, Inc. 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(2018) . It also provides means to transform new data and to carry out supervised dimensionality reduction. An implementation of the related LargeVis method of Tang et al. (2016) is also provided. This is a complete re-implementation in R (and C++, via the 'Rcpp' package): no Python installation is required. See the uwot website () for more documentation and examples.", + "License": "GPL (>= 3)", + "URL": "https://github.com/jlmelville/uwot, https://jlmelville.github.io/uwot/", + "BugReports": "https://github.com/jlmelville/uwot/issues", + "Depends": [ + "Matrix" + ], + "Imports": [ + "FNN", + "irlba", + "methods", + "Rcpp", + "RcppAnnoy (>= 0.0.17)", + "RSpectra" + ], + "Suggests": [ + "bigstatsr", + "covr", + "knitr", + "RcppHNSW", + "rmarkdown", + "rnndescent", + "testthat" + ], + "LinkingTo": [ + "dqrng", + "Rcpp", + "RcppAnnoy", + "RcppProgress" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "rmarkdown", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "James Melville [aut, cre, cph], Aaron Lun [ctb], Mohamed Nadhir Djekidel [ctb], Yuhan Hao [ctb], Dirk Eddelbuettel [ctb], Wouter van der Bijl [ctb]", + "Maintainer": "James Melville ", + "Repository": "CRAN" + }, + "vctrs": { + "Package": "vctrs", + "Version": "0.6.5", + "Source": "Repository", + "Title": "Vector Helpers", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = \"aut\"), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"data.table team\", role = \"cph\", comment = \"Radix sort based on data.table's forder() and their contribution to R's order()\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Defines new notions of prototype and size that are used to provide tools for consistent and well-founded type-coercion and size-recycling, and are in turn connected to ideas of type- and size-stability useful for analysing function interfaces.", + "License": "MIT + file LICENSE", + "URL": "https://vctrs.r-lib.org/, https://github.com/r-lib/vctrs", + "BugReports": "https://github.com/r-lib/vctrs/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "glue", + "lifecycle (>= 1.0.3)", + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "bit64", + "covr", + "crayon", + "dplyr (>= 0.8.5)", + "generics", + "knitr", + "pillar (>= 1.4.4)", + "pkgdown (>= 2.0.1)", + "rmarkdown", + "testthat (>= 3.0.0)", + "tibble (>= 3.1.3)", + "waldo (>= 0.2.0)", + "withr", + "xml2", + "zeallot" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-GB", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut], Lionel Henry [aut], Davis Vaughan [aut, cre], data.table team [cph] (Radix sort based on data.table's forder() and their contribution to R's order()), Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "viridis": { + "Package": "viridis", + "Version": "0.6.5", + "Source": "Repository", + "Type": "Package", + "Title": "Colorblind-Friendly Color Maps for R", + "Date": "2024-01-28", + "Authors@R": "c( person(\"Simon\", \"Garnier\", email = \"garnier@njit.edu\", role = c(\"aut\", \"cre\")), person(\"Noam\", \"Ross\", email = \"noam.ross@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Bob\", \"Rudis\", email = \"bob@rud.is\", role = c(\"ctb\", \"cph\")), person(\"Marco\", \"Sciaini\", email = \"sciaini.marco@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Antônio Pedro\", \"Camargo\", role = c(\"ctb\", \"cph\")), person(\"Cédric\", \"Scherer\", email = \"scherer@izw-berlin.de\", role = c(\"ctb\", \"cph\")) )", + "Maintainer": "Simon Garnier ", + "Description": "Color maps designed to improve graph readability for readers with common forms of color blindness and/or color vision deficiency. The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This package also contains 'ggplot2' bindings for discrete and continuous color and fill scales. A lean version of the package called 'viridisLite' that does not include the 'ggplot2' bindings can be found at .", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 2.10)", + "viridisLite (>= 0.4.0)" + ], + "Imports": [ + "ggplot2 (>= 1.0.1)", + "gridExtra" + ], + "Suggests": [ + "hexbin (>= 1.27.0)", + "scales", + "MASS", + "knitr", + "dichromat", + "colorspace", + "httr", + "mapproj", + "vdiffr", + "svglite (>= 1.2.0)", + "testthat", + "covr", + "rmarkdown", + "maps", + "terra" + ], + "LazyData": "true", + "VignetteBuilder": "knitr", + "URL": "https://sjmgarnier.github.io/viridis/, https://github.com/sjmgarnier/viridis/", + "BugReports": "https://github.com/sjmgarnier/viridis/issues", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "no", + "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", + "Repository": "CRAN" + }, + "viridisLite": { + "Package": "viridisLite", + "Version": "0.4.2", + "Source": "Repository", + "Type": "Package", + "Title": "Colorblind-Friendly Color Maps (Lite Version)", + "Date": "2023-05-02", + "Authors@R": "c( person(\"Simon\", \"Garnier\", email = \"garnier@njit.edu\", role = c(\"aut\", \"cre\")), person(\"Noam\", \"Ross\", email = \"noam.ross@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Bob\", \"Rudis\", email = \"bob@rud.is\", role = c(\"ctb\", \"cph\")), person(\"Marco\", \"Sciaini\", email = \"sciaini.marco@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Antônio Pedro\", \"Camargo\", role = c(\"ctb\", \"cph\")), person(\"Cédric\", \"Scherer\", email = \"scherer@izw-berlin.de\", role = c(\"ctb\", \"cph\")) )", + "Maintainer": "Simon Garnier ", + "Description": "Color maps designed to improve graph readability for readers with common forms of color blindness and/or color vision deficiency. The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This is the 'lite' version of the 'viridis' package that also contains 'ggplot2' bindings for discrete and continuous color and fill scales and can be found at .", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "hexbin (>= 1.27.0)", + "ggplot2 (>= 1.0.1)", + "testthat", + "covr" + ], + "URL": "https://sjmgarnier.github.io/viridisLite/, https://github.com/sjmgarnier/viridisLite/", + "BugReports": "https://github.com/sjmgarnier/viridisLite/issues/", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", + "Repository": "CRAN" + }, + "vroom": { + "Package": "vroom", + "Version": "1.6.5", + "Source": "Repository", + "Title": "Read and Write Rectangular Text Data Quickly", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Shelby\", \"Bearrows\", role = \"ctb\"), person(\"https://github.com/mandreyel/\", role = \"cph\", comment = \"mio library\"), person(\"Jukka\", \"Jylänki\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Mikkel\", \"Jørgensen\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The goal of 'vroom' is to read and write data (like 'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial indexing step, then reads the values lazily , so only the data you actually use needs to be read. The writer formats the data in parallel and writes to disk asynchronously from formatting.", + "License": "MIT + file LICENSE", + "URL": "https://vroom.r-lib.org, https://github.com/tidyverse/vroom", + "BugReports": "https://github.com/tidyverse/vroom/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "bit64", + "cli (>= 3.2.0)", + "crayon", + "glue", + "hms", + "lifecycle (>= 1.0.3)", + "methods", + "rlang (>= 0.4.2)", + "stats", + "tibble (>= 2.0.0)", + "tidyselect", + "tzdb (>= 0.1.1)", + "vctrs (>= 0.2.0)", + "withr" + ], + "Suggests": [ + "archive", + "bench (>= 1.1.0)", + "covr", + "curl", + "dplyr", + "forcats", + "fs", + "ggplot2", + "knitr", + "patchwork", + "prettyunits", + "purrr", + "rmarkdown", + "rstudioapi", + "scales", + "spelling", + "testthat (>= 2.1.0)", + "tidyr", + "utils", + "waldo", + "xml2" + ], + "LinkingTo": [ + "cpp11 (>= 0.2.0)", + "progress (>= 1.2.1)", + "tzdb (>= 0.1.1)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "nycflights13, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "false", + "Copyright": "file COPYRIGHTS", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3.9000", + "NeedsCompilation": "yes", + "Author": "Jim Hester [aut] (), Hadley Wickham [aut] (), Jennifer Bryan [aut, cre] (), Shelby Bearrows [ctb], https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [cph] (grisu3 implementation), Mikkel Jørgensen [cph] (grisu3 implementation), Posit Software, PBC [cph, fnd]", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" + }, + "withr": { + "Package": "withr", + "Version": "3.0.2", + "Source": "Repository", + "Title": "Run Code 'With' Temporarily Modified Global State", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = c(\"aut\", \"cre\")), person(\"Kirill\", \"Müller\", , \"krlmlr+r@mailbox.org\", role = \"aut\"), person(\"Kevin\", \"Ushey\", , \"kevinushey@gmail.com\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Winston\", \"Chang\", role = \"aut\"), person(\"Jennifer\", \"Bryan\", role = \"ctb\"), person(\"Richard\", \"Cotton\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A set of functions to run code 'with' safely and temporarily modified global state. 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Also supports XML schema validation; for 'XSLT' transformations see the 'xslt' package.", + "License": "MIT + file LICENSE", + "URL": "https://xml2.r-lib.org, https://r-lib.r-universe.dev/xml2", + "BugReports": "https://github.com/r-lib/xml2/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "cli", + "methods", + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "covr", + "curl", + "httr", + "knitr", + "magrittr", + "mockery", + "rmarkdown", + "testthat (>= 3.2.0)", + "xslt" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "SystemRequirements": "libxml2: libxml2-dev (deb), libxml2-devel (rpm)", + "Collate": "'S4.R' 'as_list.R' 'xml_parse.R' 'as_xml_document.R' 'classes.R' 'format.R' 'import-standalone-obj-type.R' 'import-standalone-purrr.R' 'import-standalone-types-check.R' 'init.R' 'nodeset_apply.R' 'paths.R' 'utils.R' 'xml2-package.R' 'xml_attr.R' 'xml_children.R' 'xml_document.R' 'xml_find.R' 'xml_missing.R' 'xml_modify.R' 'xml_name.R' 'xml_namespaces.R' 'xml_node.R' 'xml_nodeset.R' 'xml_path.R' 'xml_schema.R' 'xml_serialize.R' 'xml_structure.R' 'xml_text.R' 'xml_type.R' 'xml_url.R' 'xml_write.R' 'zzz.R'", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut], Jim Hester [aut], Jeroen Ooms [aut, cre], Posit Software, PBC [cph, fnd], R Foundation [ctb] (Copy of R-project homepage cached as example)", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, + "xtable": { + "Package": "xtable", + "Version": "1.8-4", + "Source": "Repository", + "Date": "2019-04-08", + "Title": "Export Tables to LaTeX or HTML", + "Authors@R": "c(person(\"David B.\", \"Dahl\", role=\"aut\"), person(\"David\", \"Scott\", role=c(\"aut\",\"cre\"), email=\"d.scott@auckland.ac.nz\"), person(\"Charles\", \"Roosen\", role=\"aut\"), person(\"Arni\", \"Magnusson\", role=\"aut\"), person(\"Jonathan\", \"Swinton\", role=\"aut\"), person(\"Ajay\", \"Shah\", role=\"ctb\"), person(\"Arne\", \"Henningsen\", role=\"ctb\"), person(\"Benno\", \"Puetz\", role=\"ctb\"), person(\"Bernhard\", \"Pfaff\", role=\"ctb\"), person(\"Claudio\", \"Agostinelli\", role=\"ctb\"), person(\"Claudius\", \"Loehnert\", role=\"ctb\"), person(\"David\", \"Mitchell\", role=\"ctb\"), person(\"David\", \"Whiting\", role=\"ctb\"), person(\"Fernando da\", \"Rosa\", role=\"ctb\"), person(\"Guido\", \"Gay\", role=\"ctb\"), person(\"Guido\", \"Schulz\", role=\"ctb\"), person(\"Ian\", \"Fellows\", role=\"ctb\"), person(\"Jeff\", \"Laake\", role=\"ctb\"), person(\"John\", \"Walker\", role=\"ctb\"), person(\"Jun\", \"Yan\", role=\"ctb\"), person(\"Liviu\", \"Andronic\", role=\"ctb\"), person(\"Markus\", \"Loecher\", role=\"ctb\"), person(\"Martin\", \"Gubri\", role=\"ctb\"), person(\"Matthieu\", \"Stigler\", role=\"ctb\"), person(\"Robert\", \"Castelo\", role=\"ctb\"), person(\"Seth\", \"Falcon\", role=\"ctb\"), person(\"Stefan\", \"Edwards\", role=\"ctb\"), person(\"Sven\", \"Garbade\", role=\"ctb\"), person(\"Uwe\", \"Ligges\", role=\"ctb\"))", + "Maintainer": "David Scott ", + "Imports": [ + "stats", + "utils" + ], + "Suggests": [ + "knitr", + "plm", + "zoo", + "survival" + ], + "VignetteBuilder": "knitr", + "Description": "Coerce data to LaTeX and HTML tables.", + "URL": "http://xtable.r-forge.r-project.org/", + "Depends": [ + "R (>= 2.10.0)" + ], + "License": "GPL (>= 2)", + "Repository": "CRAN", + "NeedsCompilation": "no", + "Author": "David B. Dahl [aut], David Scott [aut, cre], Charles Roosen [aut], Arni Magnusson [aut], Jonathan Swinton [aut], Ajay Shah [ctb], Arne Henningsen [ctb], Benno Puetz [ctb], Bernhard Pfaff [ctb], Claudio Agostinelli [ctb], Claudius Loehnert [ctb], David Mitchell [ctb], David Whiting [ctb], Fernando da Rosa [ctb], Guido Gay [ctb], Guido Schulz [ctb], Ian Fellows [ctb], Jeff Laake [ctb], John Walker [ctb], Jun Yan [ctb], Liviu Andronic [ctb], Markus Loecher [ctb], Martin Gubri [ctb], Matthieu Stigler [ctb], Robert Castelo [ctb], Seth Falcon [ctb], Stefan Edwards [ctb], Sven Garbade [ctb], Uwe Ligges [ctb]" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.10", + "Source": "Repository", + "Type": "Package", + "Title": "Methods to Convert R Data to YAML and Back", + "Date": "2024-07-22", + "Suggests": [ + "RUnit" + ], + "Author": "Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb], Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb], Michael Quinn [ctb], Zhian N. Kamvar [ctb], Charlie Gao [ctb]", + "Maintainer": "Shawn Garbett ", + "License": "BSD_3_clause + file LICENSE", + "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", + "URL": "https://github.com/vubiostat/r-yaml/", + "BugReports": "https://github.com/vubiostat/r-yaml/issues", + "NeedsCompilation": "yes", + "Repository": "CRAN" + }, + "zoo": { + "Package": "zoo", + "Version": "1.8-14", + "Source": "Repository", + "Date": "2025-04-09", + "Title": "S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)", + "Authors@R": "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Gabor\", family = \"Grothendieck\", role = \"aut\", email = \"ggrothendieck@gmail.com\"), person(given = c(\"Jeffrey\", \"A.\"), family = \"Ryan\", role = \"aut\", email = \"jeff.a.ryan@gmail.com\"), person(given = c(\"Joshua\", \"M.\"), family = \"Ulrich\", role = \"ctb\", email = \"josh.m.ulrich@gmail.com\"), person(given = \"Felix\", family = \"Andrews\", role = \"ctb\", email = \"felix@nfrac.org\"))", + "Description": "An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.", + "Depends": [ + "R (>= 3.1.0)", + "stats" + ], + "Suggests": [ + "AER", + "coda", + "chron", + "ggplot2 (>= 3.5.0)", + "mondate", + "scales", + "stinepack", + "strucchange", + "timeDate", + "timeSeries", + "tinyplot", + "tis", + "tseries", + "xts" + ], + "Imports": [ + "utils", + "graphics", + "grDevices", + "lattice (>= 0.20-27)" + ], + "License": "GPL-2 | GPL-3", + "URL": "https://zoo.R-Forge.R-project.org/", + "NeedsCompilation": "yes", + "Author": "Achim Zeileis [aut, cre] (), Gabor Grothendieck [aut], Jeffrey A. Ryan [aut], Joshua M. Ulrich [ctb], Felix Andrews [ctb]", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN", + "Encoding": "UTF-8" + } + } +} diff --git a/04_compositional/sccomp.qmd b/04_compositional/sccomp.qmd new file mode 100644 index 0000000..7d72668 --- /dev/null +++ b/04_compositional/sccomp.qmd @@ -0,0 +1,179 @@ +--- +title: "Celltype composition with scccomp" +author: "Harvard Chan Bioinformatics Core" +date: "`r Sys.Date()`" +format: + html: + number-sections: false + default-image-extension: svg + lightbox: true + callout-icon: false + format-links: true + toc: true + theme: sandstone + echo: true + eval: true + message: false + warning: false + code-copy: true + code-overflow: wrap + code-fold: true + code-line-numbers: true + embed-resources: true + standalone: true + html-math-method: katex + grid: + sidebar-width: 250px + body-width: 900px + margin-width: 300px + comments: + hypothesis: true +params: + project_file: ../information.R +knitr: + opts_chunk: + audodep: true + cache: false + cache.lazy: false + error: true + echo: false + fig-height: 5L + fig.retina: 2L + fig-width: 11 + message: false + tidy: true + warning: false +--- + +```{r } +#| message: false +#| warning: false +stopifnot(R.version$major >= 4) # requires R4 +if (compareVersion(R.version$minor, "3.1") < 0) warning("We recommend >= R4.3.1") +stopifnot(compareVersion(as.character(BiocManager::version()), "3.18") >= 0) +stopifnot(compareVersion(as.character(packageVersion("Seurat")), "5.0.0") >= 0) +``` + +This code is in this ![](https://img.shields.io/badge/status-draft-grey) revision. + + +```{r setup} +#| cache: false +#| message: false +#| warning: false +#| echo: false +# knitr::opts_chunk$set(echo = TRUE) +library(knitr) +# Load libraries +library(Seurat) +library(sccomp) +library(SummarizedExperiment) +library(SingleCellExperiment) +library(DEGreport) + +library(rmarkdown) +library(tidyverse) +library(data.table) +library(DT) +library(patchwork) +library(pheatmap) + +library(ggprism) +library(grafify) + +library(future) + +set.seed(1454944673L) + +ggplot2::theme_set(theme_prism(base_size = 12)) +# https://grafify-vignettes.netlify.app/colour_palettes.html +# NOTE change colors here if you wish +scale_colour_discrete <- function(...) { + scale_colour_manual(..., values = as.vector(grafify:::graf_palettes[["kelly"]])) +} + + +if (future::supportsMulticore()) { + future::plan(future::multicore) +} else { + future::plan(future::multisession) +} +``` + + +## Load object and subset + +```{r} +seurat <- readRDS("data.rds") + +subset_seurat <- subset(x = seurat, subset = condition %in% c("Ctrl", "Treat")) + +Idents(object = subset_seurat) <- "celltype" + +DefaultAssay(subset_seurat) <- "RNA" +``` + +## Sccomp + + +To test for differential cell composition we use [sccomp](https://github.com/MangiolaLaboratory/sccomp) a method for differential composition and variability analyses that jointly models data count distribution, compositionality, group-specific variability, and proportion mean–variability association, being aware of outliers. + +Our model includes condition (TN vs. cold). For each cell type we get results for the intercept and our factors. We can see the results of the fit, the effects of the factor on composition and variability. You also can see the uncertainty around those effects. In the output table, the estimate columns start with the prefix c_ indicate composition, or with v_ indicate variability (when formula_variability is set). We have not used formula_variability so we only have v_ estimates for our intercept. + +```{r} +sccomp_result <- + subset_seurat |> + sccomp_estimate( + formula_composition = ~condition, # change to the right variable + .sample = sample, + .cell_group = celltype, # change to the right variable + bimodal_mean_variability_association = TRUE, + cores = 1 + ) |> + sccomp_remove_outliers(cores = 1, verbose = FALSE) |> # Optional + sccomp_test() + + +sccomp_result +``` + +### Fold Change + +```{r} +sccomp_result |> + sccomp_proportional_fold_change( + formula_composition = ~condition, + from = "Ctrl", + to = "Treat" + ) |> + select(celltype, statement) +``` + +### Boxplot of results + +Here we see proportion of each cell type in our two groups (TN and cold7). The blue boxplots represent the posterior predictive check. If the model is likely to be descriptively adequate to the data, the blue box plot should roughly overlay with the black box plot, which represents the observed data. Dots indicate samples and outlier samples are coloured in red. Boxplots colored red indicate significant differences in proportion between our groups. + +```{r} +sccomp_result |> + sccomp_boxplot(factor = "condition") +``` + +### 1-D visualization + +A plot of estimates of differential composition (c_) on the x-axis. The error bars represent 95% credible intervals. The dashed lines represent the minimal effect that the hypothesis test is based on. An effect is labelled as significant if bigger than the minimal effect according to the 95% credible interval. We get figures for both factors in our model. + +```{r} +sccomp_result |> + plot_1D_intervals() +``` + +# Conclusion + +# R Session + +Below is the output of the R session used to generate this report. Included is information on R version, OS, and versions of packages installed and used. + +```{r sessionInfo} +# Get session information +sessionInfo() +``` From 15b4663a79277dbebbb8a30b0d56477822ed1103 Mon Sep 17 00:00:00 2001 From: Ruitong Li Date: Tue, 19 Aug 2025 11:07:47 -0400 Subject: [PATCH 2/7] update renv and also test data --- 04_compositional/propeller.qmd | 31 ++++++----- 04_compositional/renv.lock | 98 ++++++++++++++++++++++++---------- 2 files changed, 84 insertions(+), 45 deletions(-) diff --git a/04_compositional/propeller.qmd b/04_compositional/propeller.qmd index 3fd02cc..53182e6 100644 --- a/04_compositional/propeller.qmd +++ b/04_compositional/propeller.qmd @@ -72,6 +72,7 @@ library(SummarizedExperiment) library(SingleCellExperiment) library(DEGreport) library(pheatmap) +library(limma) library(tidyverse) library(data.table) @@ -115,24 +116,22 @@ sanitize_datatable <- function(df, ...) { Read in the full dataset Seurat object and subset to keep only cells from the conditions of interest (cold7 vs TN). ```{r load-data} -seurat <- readRDS("data.rds") - -subset_seurat <- subset(x = seurat, subset = condition %in% c("Ctrl", "Treat")) - -Idents(object = subset_seurat) <- "celltype" - +library(sccomp) +data("seurat_obj") +subset_seurat <- subset(x = seurat_obj, subset = sample %in% c("10x_6K", "SCP424_pbmc1","SI-GA-G6","SI-GA-H3")) +Idents(object = subset_seurat) <- "cell_group" DefaultAssay(subset_seurat) <- "RNA" # Create metadata df and factor celltype meta <- subset_seurat@meta.data -meta$celltype <- factor(meta$celltype) +meta$cell_group <- factor(meta$cell_group) ``` ## Check count numbers of cells ```{r cellnumbers} -meta$condition_sample <- paste0(meta$condition, "_", meta$sample) -table(meta$condition_sample, meta$celltype) +meta$type_sample <- paste0(meta$type, "_", meta$sample) +table(meta$type_sample, meta$cell_group) ``` ## Run propeller @@ -142,8 +141,8 @@ table(meta$condition_sample, meta$celltype) # NOTE adapt with your variables of interest propres <- propeller(subset_seurat, sample = subset_seurat$sample, - clusters = subset_seurat$celltype, - group = subset_seurat$condition + clusters = subset_seurat$cell_group, + group = subset_seurat$type ) sanitize_datatable(propres) @@ -155,8 +154,8 @@ To understand discordance with sccomp results, let's evaluate proportions and va ```{r} -props <- getTransformedProps(meta$celltype, - meta$condition_sample, +props <- getTransformedProps(meta$cell_group, + meta$type_sample, transform = "logit" ) @@ -166,11 +165,11 @@ props$Proportions ```{r extracode} #| eval: false meta_propeller <- meta %>% - group_by(condition, sample) %>% + group_by(type, sample) %>% distinct(sample) -designAS <- model.matrix(~ meta_propeller$condition) -colnames(designAS) <- c("Ctrl", "Treat") +designAS <- model.matrix(~ meta_propeller$type) +colnames(designAS) <- c("cancer", "healthy") fit <- lmFit(props$TransformedProps, designAS) fit <- eBayes(fit, robust = TRUE) diff --git a/04_compositional/renv.lock b/04_compositional/renv.lock index 28df0cf..ad932c3 100644 --- a/04_compositional/renv.lock +++ b/04_compositional/renv.lock @@ -4050,6 +4050,37 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, + "fansi": { + "Package": "fansi", + "Version": "1.0.6", + "Source": "Repository", + "Title": "ANSI Control Sequence Aware String Functions", + "Description": "Counterparts to R string manipulation functions that account for the effects of ANSI text formatting control sequences.", + "Authors@R": "c( person(\"Brodie\", \"Gaslam\", email=\"brodie.gaslam@yahoo.com\", role=c(\"aut\", \"cre\")), person(\"Elliott\", \"Sales De Andrade\", role=\"ctb\"), person(family=\"R Core Team\", email=\"R-core@r-project.org\", role=\"cph\", comment=\"UTF8 byte length calcs from src/util.c\" ))", + "Depends": [ + "R (>= 3.1.0)" + ], + "License": "GPL-2 | GPL-3", + "URL": "https://github.com/brodieG/fansi", + "BugReports": "https://github.com/brodieG/fansi/issues", + "VignetteBuilder": "knitr", + "Suggests": [ + "unitizer", + "knitr", + "rmarkdown" + ], + "Imports": [ + "grDevices", + "utils" + ], + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "Collate": "'constants.R' 'fansi-package.R' 'internal.R' 'load.R' 'misc.R' 'nchar.R' 'strwrap.R' 'strtrim.R' 'strsplit.R' 'substr2.R' 'trimws.R' 'tohtml.R' 'unhandled.R' 'normalize.R' 'sgr.R'", + "NeedsCompilation": "yes", + "Author": "Brodie Gaslam [aut, cre], Elliott Sales De Andrade [ctb], R Core Team [cph] (UTF8 byte length calcs from src/util.c)", + "Maintainer": "Brodie Gaslam ", + "Repository": "CRAN" + }, "farver": { "Package": "farver", "Version": "2.1.2", @@ -8479,44 +8510,45 @@ }, "sccomp": { "Package": "sccomp", - "Version": "2.0.0", - "Source": "Bioconductor", - "Title": "Tests differences in cell-type proportion for single-cell data, robust to outliers", - "Authors@R": "c(person(\"Stefano\", \"Mangiola\", email = \"mangiolastefano@gmail.com\", role = c(\"aut\", \"cre\")) )", - "Description": "A robust and outlier-aware method for testing differences in cell-type proportion in single-cell data. This model can infer changes in tissue composition and heterogeneity, and can produce realistic data simulations based on any existing dataset. This model can also transfer knowledge from a large set of integrated datasets to increase accuracy further.", + "Version": "2.1.17", + "Source": "GitHub", + "Type": "Package", + "Title": "Differential Composition and Variability Analysis for Single-Cell Data", + "Date": "2024-01-15", + "Authors@R": "c(person(\"Stefano\", \"Mangiola\", email = \"stefano.mangiola@unimelb.edu.au\", role = c(\"aut\", \"cre\")), person(\"Alexandra J.\", \"Roth-Schulze\", role = \"aut\"), person(\"Marie\", \"Trussart\", role = \"aut\"), person(\"Enrique\", \"Zozaya-Valdés\", role = \"aut\"), person(\"Mengyao\", \"Ma\", role = \"aut\"), person(\"Zijie\", \"Gao\", role = \"aut\"), person(\"Alan F.\", \"Rubin\", role = \"aut\"), person(\"Terence P.\", \"Speed\", role = \"aut\"), person(\"Heejung\", \"Shim\", role = \"aut\"), person(\"Anthony T.\", \"Papenfuss\", role = \"aut\"))", + "Description": "Comprehensive R package for differential composition and variability analysis in single-cell RNA sequencing, CyTOF, and microbiome data. Provides robust Bayesian modeling with outlier detection, random effects, and advanced statistical methods for cell type proportion analysis. Features include probabilistic outlier identification, mixed-effect modeling, differential variability testing, and comprehensive visualization tools. Perfect for cancer research, immunology, developmental biology, and single-cell genomics applications.", "License": "GPL-3", - "URL": "https://github.com/MangiolaLaboratory/sccomp", - "BugReports": "https://github.com/MangiolaLaboratory/sccomp/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", - "RoxygenNote": "7.3.3", + "RoxygenNote": "7.3.2", "Depends": [ - "R (>= 4.3.0)" + "R (>= 4.3.0)", + "instantiate (>= 0.2.3)" ], "Imports": [ - "instantiate (>= 0.2.3)", "stats", - "SingleCellExperiment", - "parallel", + "boot", + "utils", + "scales", + "lifecycle", + "rlang", + "tidyselect", + "magrittr", + "crayon", + "cli", + "fansi", "dplyr", "tidyr", "purrr", - "magrittr", - "rlang", "tibble", - "boot", - "lifecycle", - "tidyselect", - "utils", "ggplot2", "ggrepel", "patchwork", "forcats", "readr", - "scales", "stringr", "glue", - "crayon" + "SingleCellExperiment" ], "Suggests": [ "knitr", @@ -8526,24 +8558,32 @@ "markdown", "loo", "prettydoc", + "SeuratObject", "tidyseurat", "tidySingleCellExperiment", "bayesplot", "posterior" ], "Additional_repositories": "https://mc-stan.org/r-packages/", - "SystemRequirements": "CmdStan (https://mc-stan.org/users/interfaces/cmdstan)", + "SystemRequirements": "CmdStan (https://mc-stan.org/users/interfaces/cmdstan), C++14", "biocViews": "Bayesian, Regression, DifferentialExpression, SingleCell, Metagenomics, FlowCytometry, Spatial", "LazyData": "true", "VignetteBuilder": "knitr", - "git_url": "https://git.bioconductor.org/packages/sccomp", - "git_branch": "RELEASE_3_21", - "git_last_commit": "a466882", - "git_last_commit_date": "2025-04-15", - "Repository": "Bioconductor 3.21", - "NeedsCompilation": "no", - "Author": "Stefano Mangiola [aut, cre]", - "Maintainer": "Stefano Mangiola " + "URL": "https://github.com/MangiolaLaboratory/sccomp", + "BugReports": "https://github.com/MangiolaLaboratory/sccomp/issues", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/testthat/snapshot/parallel": "true", + "Config/testthat/snapshot/parallel/workers": "2", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteRepo": "sccomp", + "RemoteUsername": "MangiolaLaboratory", + "RemoteRef": "HEAD", + "RemoteSha": "b9f62302fc54bca23266bd70dc0828b02e73dfeb", + "NeedsCompilation": "no", + "Author": "Stefano Mangiola [aut, cre], Alexandra J. Roth-Schulze [aut], Marie Trussart [aut], Enrique Zozaya-Valdés [aut], Mengyao Ma [aut], Zijie Gao [aut], Alan F. Rubin [aut], Terence P. Speed [aut], Heejung Shim [aut], Anthony T. Papenfuss [aut]", + "Maintainer": "Stefano Mangiola " }, "sctransform": { "Package": "sctransform", From bf316743054df9839488629e7dbede58943e9711 Mon Sep 17 00:00:00 2001 From: lijin0303 Date: Tue, 19 Aug 2025 15:10:36 +0000 Subject: [PATCH 3/7] Style code (GHA) --- 04_compositional/propeller.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/04_compositional/propeller.qmd b/04_compositional/propeller.qmd index 53182e6..db5250b 100644 --- a/04_compositional/propeller.qmd +++ b/04_compositional/propeller.qmd @@ -118,7 +118,7 @@ Read in the full dataset Seurat object and subset to keep only cells from the co ```{r load-data} library(sccomp) data("seurat_obj") -subset_seurat <- subset(x = seurat_obj, subset = sample %in% c("10x_6K", "SCP424_pbmc1","SI-GA-G6","SI-GA-H3")) +subset_seurat <- subset(x = seurat_obj, subset = sample %in% c("10x_6K", "SCP424_pbmc1", "SI-GA-G6", "SI-GA-H3")) Idents(object = subset_seurat) <- "cell_group" DefaultAssay(subset_seurat) <- "RNA" From 5c9861f49748e79d78c04426883ca0db6e7884ba Mon Sep 17 00:00:00 2001 From: Ruitong Li Date: Tue, 26 Aug 2025 09:24:04 -0400 Subject: [PATCH 4/7] updated properller qmd --- 04_compositional/propeller.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/04_compositional/propeller.qmd b/04_compositional/propeller.qmd index db5250b..53182e6 100644 --- a/04_compositional/propeller.qmd +++ b/04_compositional/propeller.qmd @@ -118,7 +118,7 @@ Read in the full dataset Seurat object and subset to keep only cells from the co ```{r load-data} library(sccomp) data("seurat_obj") -subset_seurat <- subset(x = seurat_obj, subset = sample %in% c("10x_6K", "SCP424_pbmc1", "SI-GA-G6", "SI-GA-H3")) +subset_seurat <- subset(x = seurat_obj, subset = sample %in% c("10x_6K", "SCP424_pbmc1","SI-GA-G6","SI-GA-H3")) Idents(object = subset_seurat) <- "cell_group" DefaultAssay(subset_seurat) <- "RNA" From d9dd56ea82d2c257973d941b3722090f2d923795 Mon Sep 17 00:00:00 2001 From: Ruitong Li Date: Tue, 26 Aug 2025 09:24:40 -0400 Subject: [PATCH 5/7] properller action file --- .github/workflows/run_propeller.yml | 74 +++++++++++++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 .github/workflows/run_propeller.yml diff --git a/.github/workflows/run_propeller.yml b/.github/workflows/run_propeller.yml new file mode 100644 index 0000000..e5d80a6 --- /dev/null +++ b/.github/workflows/run_propeller.yml @@ -0,0 +1,74 @@ +name: Propeller compositional analysis + +on: + push: + branches: [main] + paths: + - '04_compositional/propeller.qmd' + pull_request: + branches: [main] + paths: + - '04_compositional/propeller.qmd' + workflow_dispatch: + +jobs: + r-propeller: + runs-on: ubuntu-22.04 + + env: + RENV_PATHS_ROOT: ~/.local/share/renv # persistent cache location + + steps: + - name: Checkout code + uses: actions/checkout@v4 + + - name: Install pandoc + run: sudo apt-get update && sudo apt-get install -y pandoc + + - name: Set up R + uses: r-lib/actions/setup-r@v2 + + - name: Install system dependencies for R packages + run: | + sudo apt-get update + sudo apt-get install -y build-essential libcurl4-openssl-dev libssl-dev libxml2-dev libgit2-dev libmagick++-dev libharfbuzz-dev libfribidi-dev libglpk-dev + shell: bash + + - name: Cache R packages (renv) + uses: actions/cache@v4 + with: + path: ${{ env.RENV_PATHS_ROOT }} + key: ${{ runner.os }}-renv-${{ hashFiles('04_compositional/renv.lock') }} + restore-keys: | + ${{ runner.os }}-renv- + + - name: Set repositories + run: Rscript ubuntu.R + + - name: Restore environment from renv.lock + run: | + install.packages("renv", repos = "https://cloud.r-project.org") + renv::restore(prompt = FALSE, lockfile = "04_compositional/renv.lock") + shell: Rscript {0} + + - name: Set up Quarto + uses: quarto-dev/quarto-actions/setup@v2 + + - name: Run propeller report + id: render_qmd + run: | + cd 04_compositional + quarto render propeller.qmd + shell: bash + + - name: Deploy HTML to gh-pages + if: success() + run: | + git config --global user.name "github-actions[bot]" + git config --global user.email "github-actions[bot]@users.noreply.github.com" + git fetch origin gh-pages || git checkout --orphan gh-pages + git switch gh-pages || git checkout -b gh-pages + git add 04_compositional/propeller.html + git commit -m "Deploy propeller.html [skip ci]" || echo "No changes to commit" + git push origin gh-pages + shell: bash From dbb420d4504edb32511f935326bb8298305fe9cb Mon Sep 17 00:00:00 2001 From: Ruitong Li Date: Tue, 26 Aug 2025 10:39:32 -0400 Subject: [PATCH 6/7] Fix fig-height and fig.retina values in propeller.qmd --- 04_compositional/propeller.qmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/04_compositional/propeller.qmd b/04_compositional/propeller.qmd index 53182e6..be7465d 100644 --- a/04_compositional/propeller.qmd +++ b/04_compositional/propeller.qmd @@ -37,8 +37,8 @@ knitr: cache.lazy: false error: true echo: false - fig-height: 5L - fig.retina: 2L + fig-height: 5 + fig.retina: 2 fig-width: 11 message: false tidy: true From 88c5cb88e95d42f4a34ed683e151ea72d4545737 Mon Sep 17 00:00:00 2001 From: lijin0303 Date: Tue, 26 Aug 2025 14:43:48 +0000 Subject: [PATCH 7/7] Style code (GHA) --- 04_compositional/propeller.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/04_compositional/propeller.qmd b/04_compositional/propeller.qmd index be7465d..7e5f73d 100644 --- a/04_compositional/propeller.qmd +++ b/04_compositional/propeller.qmd @@ -118,7 +118,7 @@ Read in the full dataset Seurat object and subset to keep only cells from the co ```{r load-data} library(sccomp) data("seurat_obj") -subset_seurat <- subset(x = seurat_obj, subset = sample %in% c("10x_6K", "SCP424_pbmc1","SI-GA-G6","SI-GA-H3")) +subset_seurat <- subset(x = seurat_obj, subset = sample %in% c("10x_6K", "SCP424_pbmc1", "SI-GA-G6", "SI-GA-H3")) Idents(object = subset_seurat) <- "cell_group" DefaultAssay(subset_seurat) <- "RNA"