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lpantano merged 2 commits into from
Apr 4, 2025
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bump to 0.4.4 #141

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7688f37
bump to 0.4.4
lpantano Apr 4, 2025
4d84c4d
update news
lpantano Apr 4, 2025
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2 changes: 1 addition & 1 deletion DESCRIPTION
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@@ -1,7 +1,7 @@
Package: bcbioR
Type: Package
Title: Templates and functions to guide downstream analysis and data interpretation
Version: 0.4.3
Version: 0.4.4
Authors@R: person("Pantano", "Lorena", , "lorena.pantano@gmail.com",
role = c("aut", "cre"))
Description: Collaborative code repository at the Harvard Chan Bioinformatics Core.
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30 changes: 30 additions & 0 deletions NEWS.md
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# bcbioR 0.4.4

init QC single cell adding init file for params for single QC #123
on disk seurat object How to make a Seurat object with BPcells-good for big objects #128
add gene name to count matrix Add gene name to counts files rnaseq-reports#8
Add style checks to rnaseq and singlecell repositories
Restructure singlecell readmes

# bcbioR 0.4.3

migrate rnaseq templates to its own repo #120
add HD visium QC #101
add HD visum clustering #102
include code to generate files for DEGpattern #116
double code for single cell #130
adapt to QC to ATACseq #133
fix error in names #132
fix GSEA rnaseq error and styling code bcbio/rnaseq-reports#2

# bcbioR 0.4.2

Filter genes according biotype or gene name #117
Add Visium HD QC #101 #115
Add degPattern template #97
Collapse multiple params files #65
Add rmaseq library links #60
Fix version comparison #104
Save log object in sc data #105
More docs for clusters ids #106

# bcbioR 0.4.1

- in DEG.Rmd, write expression table only once https://github.com/bcbio/bcbioR/issues/63
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8 changes: 4 additions & 4 deletions R/helpers.R
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Expand Up @@ -212,11 +212,11 @@ copy_templates <- function(path, pipeline, org=NULL){
names(repos)="rnaseq-reports"
}else if(pipeline=="singlecell"){
parts = c("templates/singlecell")
# repos = "https://github.com/bcbio/singlecell-reports"
# names(repos)="singlecell-reports"
repos = "https://github.com/bcbio/singlecell-reports/archive/refs/heads/main.zip"
names(repos)="singlecell-reports"
apps=c(apps, scRNAseq_qc="https://github.com/hbc/scRNAseq_qc_app/archive/refs/heads/main.zip")
}else if(pipeline=="singlecell_delux"){
parts = c("templates/singlecell_delux")
# }else if(pipeline=="singlecell_delux"){
# parts = c("templates/singlecell_delux")
}else if(pipeline=="multiomics"){
parts = c("templates/multiomics")
}else if(pipeline=="spatial"){
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45 changes: 23 additions & 22 deletions README.md
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Expand Up @@ -43,28 +43,29 @@ bcbio_templates(type="rnaseq", outpath="/path/to/analysis/folder/reports")

## Supported analyses

- base/reports/example.Rmd: ![](https://img.shields.io/badge/status-stable-green)
- [rnaseq-reports](https://github.com/bcbio/rnaseq-reports):
- 01_quality_assessment/QC.Rmd: ![](https://img.shields.io/badge/status-stable-green)
- 02_differential_expression/DEG.Rmd: ![](https://img.shields.io/badge/status-stable-green)
- 03_functional/Nonmodel_Organism_Pathway_Analysis.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
- 03_functional/GSVA.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
- 03_functional/Immune-deconvolution.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
- 03_comparative/Pair-wise-comparison-analysis.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
- 03_comparative/Intersections.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
- 04_gene_patterns/WGCNA.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
- 05_gene_patterns/DEGpattern.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
- [singlecell/01_quality_assessment/scRNA_QC.Rmd](singlecell/01_quality_assessment/scATAC_QC.Rmd): ![](https://img.shields.io/badge/status-stable-green)
- [singlecell/01_quality_assessment/scATAC_QC.Rmd](singlecell/01_quality_assessment/scATAC_QC.Rmd): ![](https://img.shields.io/badge/status-draft-grey)
- [singlecell/02_differential_expression/scRNA_MAST.Rmd](singlecell/02_differential_expression/scRNA_MAST.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)
- [singlecell/02_differential_expression/scRNA_pseudobulk.Rmd](singlecell/02_differential_expression/scRNA_pseudobulk.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)
- [singlecell/04_compositional/propeller.Rmd](singlecell/04_compositional/propeller.Rmd): ![](https://img.shields.io/badge/status-draft-grey)
- [singlecell/04_compositional/sccomp.Rmd](singlecell/04_compositional/sccomp.Rmd): ![](https://img.shields.io/badge/status-draft-grey)
- [singlecell_delux/01_CellToCell/cellchat.Rmd](singlecell_delux/01_CellToCell/cellchat.Rmd): ![](https://img.shields.io/badge/status-draft-grey)
- [chipseq/02_diffbind/diffbind.Rmd](chipseq/02_diffbind/diffbind.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)
- [chipseq/01_quality_assessment/QC.Rmd](chipseq/01_quality_assessment/QC.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)
- [spatial/visium/01_quality_assessment/qc.Rmd](spatial/visium/01_quality_assessment/qc.Rmd): ![](https://img.shields.io/badge/status-draft-grey)
- [spatial/cosmx/01_quality_assessment/QC.Rmd](spatial/cosmx/01_quality_assessment/QC.Rmd): ![](https://img.shields.io/badge/status-draft-grey)
- base/reports/example.Rmd: ![](https://img.shields.io/badge/status-stable-green)
- [rnaseq-reports](https://github.com/bcbio/rnaseq-reports):
- 01_quality_assessment/QC.Rmd ![](https://img.shields.io/badge/status-stable-green)
- 02_differential_expression/DEG.Rmd ![](https://img.shields.io/badge/status-stable-green)
- 03_functional/Nonmodel_Organism_Pathway_Analysis.Rmd ![](https://img.shields.io/badge/status-alpha-yellow)
- 03_functional/GSVA.Rmd ![](https://img.shields.io/badge/status-alpha-yellow)
- 03_functional/Immune-deconvolution.Rmd ![](https://img.shields.io/badge/status-alpha-yellow)
- 03_comparative/Pair-wise-comparison-analysis.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
- 03_comparative/Intersections.Rmd ![](https://img.shields.io/badge/status-alpha-yellow)
- 04_gene_patterns/WGCNA.Rmd ![](https://img.shields.io/badge/status-alpha-yellow)
- 05_gene_patterns/DEGpattern.Rmd ![](https://img.shields.io/badge/status-alpha-yellow)
- [single-cell](https://github.com/bcbio/rnaseq-reports)
- singlecell/01_quality_assessment/scRNA_QC.Rmd
- 01_quality_assessment/scATAC_QC.Rmd ![](https://img.shields.io/badge/status-draft-grey)
- 02_differential_expression/scRNA_MAST.Rmd ![](https://img.shields.io/badge/status-alpha-yellow)
- 02_differential_expression/scRNA_pseudobulk.Rmd ![](https://img.shields.io/badge/status-alpha-yellow)
- singlecell/04_compositional/propeller.Rmd ![](https://img.shields.io/badge/status-draft-grey)
- 04_compositional/sccomp.Rmd ![](https://img.shields.io/badge/status-draft-grey)
- 05_signaling/cellchat.Rmd: ![](https://img.shields.io/badge/status-draft-grey)
- [chipseq/02_diffbind/diffbind.Rmd](inst/templates/chipseq/02_diffbind/diffbind.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)
- [chipseq/01_quality_assessment/QC.Rmd](inst/templates/chipseq/01_quality_assessment/QC.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)
- [spatial/visium/01_quality_assessment/qc.Rmd](inst/templates/spatial/visium/01_quality_assessment/qc.Rmd): ![](https://img.shields.io/badge/status-draft-grey)
- [spatial/cosmx/01_quality_assessment/QC.Rmd](inst/templates/spatial/cosmx/01_quality_assessment/QC.Rmd): ![](https://img.shields.io/badge/status-draft-grey)

### Discover more…

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