R Observatory: Metrics for gcpca version 0.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

gcpca

0.0.1Package record

Generalized Contrastive Principal Component Analysis

0packages depend

2.1Kdownloads / year

60.2%test coverage

13/13flavors OK

Overview

About

Maintained by Eliezyer de OliveiraCRAN page ↗GitHub ↗Issues ↗

Implements dense and sparse generalized contrastive principal component analysis (gcPCA) with S3 fit objects and methods for prediction, summaries, and plotting. The gcPCA is a hyperparameter-free method for comparing high-dimensional datasets collected under different experimental conditions to reveal low-dimensional patterns enriched in one condition compared to the other. Method details are described in de Oliveira, Garg, Hjerling-Leffler, Batista-Brito, and Sjulson (2025) doi:10.1371/journal.pcbi.1012747.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("gcpca", 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("SjulsonLab/generalized_contrastive_PCA")

Development version from SjulsonLab/generalized_contrastive_PCA. 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-gcpca

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-gcpca

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-gcpca

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 53 s · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK6 OK2026-04-02

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.0.1

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 12 (1 internal)includes a package overview page
Examples that run: 100%2 run in a plain check
Exported functions with examples: 50%
Documented parameters: 94%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.1K

CRAN downloads in the past year

Rank #19,732 · ~6/day · ~177/mo

Releases R versions

Daily download trend is not available in this view yet.

22330 days

67490 days

2.1K1 year

Compare downloads with other packages →

Also on41 r2u5 autocran

How downloads are counted

Repository

sjulsonlab/generalized_contrastive_pca ↗Organization: SjulsonLab

29Stars

2Forks

0Open issues

0Open PRs

3Releases

144Commits

8Commit identities

contrastivedata-analysisdimensionality-reductionneuroscienceomics-analysis

License file reads as GPL-3.0 · 144 commits · Last activity 2026-03-29 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 124
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-08-06 · 212026-07-10 · 29

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/sjulsonlab/generalized_contrastive_pca on 2026-10-22.

Continuous integration (1)

GitHub Actions

Lint, format, editor (2)

VS CodeJetBrains/.idea

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Installing gcpca adds no packages beyond those that come with R.

Depends (0)

none

Imports (2)

graphicsstats

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Eliezyer de Oliveira

Author, Maintainer since 0.0.1 (2026)

Releases (1)

R
R 4.6.0 released · 2026-04-24
0.0.1Latest
record
2026-04-01 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-04-01
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Download size: 13 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("gcpca")

Format

de Oliveira, E. (2026). gcpca: Generalized Contrastive Principal Component Analysis (Version 0.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.gcpca

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 gcpca version 0.0.1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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