R Observatory: Metrics for RCPA version 0.2.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

RCPA

0.2.9

Consensus Pathway Analysis

0packages depend

5.8Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Ha NguyenFirst published 2023-05-1111 releasesCRAN page ↗GitHub ↗

Provides a set of functions to perform pathway analysis and meta-analysis from multiple gene expression datasets, as well as visualization of the results. This package wraps functionality from the following packages: Ritchie et al. (2015) doi:10.1093/nar/gkv007, Love et al. (2014) doi:10.1186/s13059-014-0550-8, Robinson et al. (2010) doi:10.1093/bioinformatics/btp616, Korotkevich et al. (2016) arxiv:10.1101/060012, Efron et al. (2015) https://CRAN.R-project.org/package=GSA, and Gu et al. (2012) https://CRAN.R-project.org/package=CePa.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("RCPA", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("tinnlab/RCPA")

Development version from tinnlab/RCPA. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-rcpa

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

1ERROR12OK

Failing flavors

ERROR r-oldrel-windows-x86_64

Slowest check: 7.4 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

25

Dependencies · direct

Check history

ERROR2026-08-09
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-14
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-10
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 15 earlier snapshots

OK2026-07-08
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
11 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE
OK2026-04-28
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-24
12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-11
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-25
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-12
12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 11%
Documented parameters: 92%
Return-value docs: 100%
References docs: 0%

Downloads

5.8K

CRAN downloads in the past year

Rank #6,090 · ~16/day · ~484/mo

Releases R versions

Daily download trend is not available in this view yet.

28730 days

1.3K90 days

5.8K1 year

Compare downloads with other packages →

Also on168 r2u

Repository

GitHub ↗ tinnlab/rcpa

1Stars

2Forks

1Open issues

0Open PRs

0Releases

283Commits

8Contributors

283 commits · Last activity 2026-07-14

Stars over time

2024-05-11 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 1 family in the upstream repository

Checks run against github.com/tinnlab/rcpa on 2026-08-23.

Lint, format, editor (2)

RStudio projectJetBrains/.idea

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

39 external dependencies (excludes base and recommended)

Depends (6)

R >= 4.0tidyr dplyr ggplot2utilsstats

Imports (20)

AnnotationDbi SummarizedExperiment BiocManager Biobase DESeq2 GEOquery edgeR limma stringr ggnewscale ggrepel graph httr rlang ggpattern scales RobustRankAggregmethodsjsonlite IRdisplay

LinkingTo (0)

none

Suggests (17)

knitr rmarkdown markdown testthat ROntoTools fgsea GSA CePa meta png ggvenn RCurl XML S4Vectors hgu133plus2.db org.Hs.eg.db oligo

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Ha Nguyen

Author, Maintainer · added in 0.1.2

Authors (3)

Ha Nguyen

Author, Maintainer · added in 0.1.2

Phi Bya

Author · added in 0.2.3

Zeynab Maghsoudi

Author

Funders (1)

Tin Nguyen

Funder

Listed in earlier versions (1)

Phi Hung Bya

no longer listed · 0.1.0 to 0.2.2

Package Timeline

11 releases. Pick two to compare their code metrics. R releases are shown for context.

0.2.9Latest
2026-07-14 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.2.8
2025-09-15 · diff ↗
0.2.7
2025-07-28 · diff ↗
0.2.6
2025-04-30 · diff ↗
unarchivedReturned to CRAN
2025-04-30
R
R 4.5.0 released · 2025-04-11
archivedRemoved from CRAN
2025-04-04
policy violation On Internet access
0.2.5
2024-11-06 · diff ↗
unarchivedReturned to CRAN
2024-11-06
archivedRemoved from CRAN
2024-10-10
policy violation On Internet access
0.2.3
2024-07-03 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.2.2
2024-04-15 · diff ↗
0.2.1
2023-11-30 · diff ↗
0.1.2
2023-11-21 · diff ↗

Show 7 earlier events

unarchivedReturned to CRAN
2023-11-21
archivedRemoved from CRAN
2023-11-12
policy violation On Internet access
0.1.1
2023-07-13 · diff ↗
unarchivedReturned to CRAN
2023-07-13
archivedRemoved from CRAN
2023-05-25
issues were not corrected in time Not using suggested packages conditionally
0.1.0
2023-05-11
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-05-11
Total releases: 11 / 3 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0
Download size: 4.8 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("RCPA")

Format

Nguyen, H., Bya, P., Maghsoudi, Z., & Nguyen, T. (2026). RCPA: Consensus Pathway Analysis (Version 0.2.9) [Computer software]. https://doi.org/10.32614/CRAN.package.RCPA

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for RCPA version 0.2.9 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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