R Observatory: Metrics for ProteinPCA version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ProteinPCA

0.1.1

Principal Component Analysis (PCA) Tool on Protein Expression Data

0packages depend

5.3Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Paul Angelo C. ManlapazFirst published 2025-04-122 releasesCRAN page ↗

Analysis of protein expression data can be done through Principal Component Analysis (PCA), and this R package is designed to streamline the analysis. This package enables users to perform PCA and it generates biplot and scree plot for advanced graphical visualization. Optionally, it supports grouping/clustering visualization with PCA loadings and confidence ellipses. With this R package, researchers can quickly explore complex protein datasets, interpret variance contributions, and visualize sample clustering through intuitive biplots. For more details, see Jolliffe (2001) doi:10.1007/b98835, Gabriel (1971) doi:10.1093/biomet/58.3.453, Zhang et al. (2024) doi:10.1038/s41467-024-53239-9, and Anandan et al. (2022) doi:10.1038/s41598-022-07781-5.

Install

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

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

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

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-proteinpca

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

# 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-ProteinPCA

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-ProteinPCA

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 1.4 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

3

Dependencies · direct

Check history

NOTE2026-07-11
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: 100%
References docs: 100%

Downloads

5.3K

CRAN downloads in the past year

Rank #10,707 · ~14/day · ~440/mo

Releases R versions

Daily download trend is not available in this view yet.

19230 days

91390 days

5.3K1 year

Compare downloads with other packages →

Also on105 r2u18 autocran

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (3)

statsggplot2 gridExtra

LinkingTo (0)

none

Suggests (2)

testthatMASS

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Paul Angelo C. Manlapaz

Author, Maintainer

Authors (1)

Paul Angelo C. Manlapaz

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.1.1Latest
2025-08-22 · current release · diff ↗
0.1.0
2025-04-12
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-04-12
Total releases: 2 / 1 yrs
License: GPL-3 OSI
Download size: 4.0 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ProteinPCA")

Format

Manlapaz, P. A. C. (2025). ProteinPCA: Principal Component Analysis (PCA) Tool on Protein Expression Data (Version 0.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.ProteinPCA

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 ProteinPCA version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-08-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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