r4projects

r4projects is an R package for organizing bioinformatics projects and handling common research-support tasks around publication tracking, profile scraping, package metadata lookup, and lightweight visualization.

The package is designed for day-to-day academic workflows rather than for a single analysis pipeline. It combines project scaffolding utilities with helper functions that pull information from Google Scholar, PubMed, GitHub, GitLab, and Gitee.

Installation

Install the released source from GitHub:

remotes::install_github("jaspershen-lab/r4projects")

Load the package:

library(r4projects)

What the package does

r4projects currently covers five practical areas.

1. Project organization

The package can create a standard directory layout for an R-based bioinformatics project.

create_project_organization()
get_project_wd()
openwd()
ignore_large_files()

Typical folders created by create_project_organization() include:

• 1_code
• 2_data
• 3_data_analysis
• 4_manuscript
• 5_summary

This is useful when you want a repeatable project structure for exploratory analysis, manuscript preparation, and summary reporting.

2. Google Scholar helpers

The package can cache and parse Google Scholar pages to retrieve profile and publication information.

profile <- request_profile(user_id = "3TK9yz8AAAAJ")
citations <- request_citation(user_id = "3TK9yz8AAAAJ")
pubs <- request_publications(user_id = "3TK9yz8AAAAJ")
paper <- request_publication_info(
  user_id = "3TK9yz8AAAAJ",
  pub_id = "0EnyYjriUFMC"
)

Related functions:

• craw_or_load_page()
• craw_or_load_publication()
• request_profile()
• request_citation()
• draw_citation_history()
• request_coauthors()
• request_publications()
• request_publication_info()

3. PubMed helpers

The package includes helpers for linking Google Scholar entries to PubMed and extracting PubMed metadata.

pmid <- convert_gs_pub_id2pmid(
  gs_user_id = "3TK9yz8AAAAJ",
  gs_pub_id = "0EnyYjriUFMC"
)

pubmed_info <- request_pubmed_publication_info(pmid = pmid)

These functions are useful when you want to recover author affiliations, identifiers, abstracts, or other structured paper metadata.

4. GitHub and package metadata helpers

The package can collect simple GitHub profile information and package metadata from repository hosting platforms.

gh_profile <- require_github_profile("jaspershen")
gh_activity <- require_github_contribution_activity("jaspershen")
pkg_info <- require_package_info("jaspershen/laggedcor", from = "github")

There is also a convenience installer for packages hosted on GitHub, GitLab, or Gitee:

install_fastgit("jaspershen/laggedcor", from = "github")

5. Visualization and academic website support

The package includes plotting helpers and functions used in personal or lab website workflows.

draw_citation_history(user_id = "3TK9yz8AAAAJ")
generate_collaborator_map(gs_user_id = "3TK9yz8AAAAJ")

Additional helpers include:

• color_palette()
• theme_shenlab()
• update_packages_tidymass_org()

Example workflow

A minimal workflow for a new analysis project might look like this:

library(r4projects)

create_project_organization()
setwd(get_project_wd())

pubs <- request_publications(user_id = "3TK9yz8AAAAJ")
plot <- draw_citation_history(user_id = "3TK9yz8AAAAJ")

Exported functions

Main exported functions in the package:

• color_palette()
• convert_gs_pub_id2pmid()
• craw_or_load_page()
• craw_or_load_publication()
• create_project_organization()
• draw_citation_history()
• fuzzy_match()
• generate_collaborator_map()
• get_os()
• get_project_wd()
• ignore_large_files()
• install_fastgit()
• openwd()
• r4projects_logo()
• r4projects_packages()
• request_citation()
• request_coauthors()
• request_profile()
• request_publication_info()
• request_publications()
• request_pubmed_publication_info()
• require_github_contribution_activity()
• require_github_profile()
• require_package_info()
• show_progresser()
• theme_shenlab()
• update_packages_tidymass_org()

Notes

• Several functions rely on live web pages and may break if upstream page structures change.
• Google Scholar scraping should be used conservatively because aggressive requests may be throttled.
• Some functions are tailored to the author's existing workflow and may be most useful as lightweight utilities rather than general APIs.

Documentation website

The pkgdown site for the package is intended to be published at:

https://jaspershen-lab.github.io/r4projects/

To rebuild the site locally:

pkgdown::build_site()

Author

Xiaotao Shen
Email: xiaotao.shen@outlook.com