PCAPAM50

1.0.3

Enhanced 'PAM50' Subtyping of Breast Cancer

0packages depend

2.2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Praveen-Kumar Raj-KumarFirst published 2024-07-084 releasesCRAN page ↗

Accurate classification of breast cancer tumors based on gene expression data is not a trivial task, and it lacks standard practices.The 'PAM50' classifier, which uses 50 gene centroid correlation distances to classify tumors, faces challenges with balancing estrogen receptor (ER) status and gene centering. The 'PCAPAM50' package leverages principal component analysis and iterative 'PAM50' calls to create a gene expression-based ER-balanced subset for gene centering, avoiding the use of protein expression-based ER data resulting into an enhanced Breast Cancer subtyping.

Install

R (CRAN)Ubuntu (r2u)

install.packages("PCAPAM50", 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-pcapam50

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

13OK

Slowest check: 3.4 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.09

not tracked

Coverage

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 25%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 0%

Downloads

2.2K

CRAN downloads in the past year

Rank #18,711 · ~6/day · ~183/mo

Releases R versions

Daily download trend is not available in this view yet.

18830 days

61490 days

2.2K1 year

Compare downloads with other packages →

Also on110 r2u

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (4)

BiobaselatticeComplexHeatmap impute

LinkingTo (0)

none

Suggests (3)

testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (8)

Maintainer (1)

Praveen-Kumar Raj-Kumar

Author, Maintainer, Copyright holder

Authors (8)

Praveen-Kumar Raj-Kumar

Author, Maintainer, Copyright holder

Boyi Chen

Author · added in 1.0.1

Tyler Hohenstein

Author · added in 1.0.1

Hai Hu

Author, Copyright holder

Ming-Wen Hu

Author · added in 1.0.1

Xiaoying Lin

Author, Copyright holder · added in 1.0.1

Jianfang Liu

Author

Craig D. Shriver

Author

Praveen-Kumar Raj-Kumar

Author, Maintainer, Copyright holder

Hai Hu

Author, Copyright holder

Xiaoying Lin

Author, Copyright holder · added in 1.0.1

Listed in earlier versions (3)

Jeffrey A. Hooke

no longer listed · 1.0.0

Albert J. Kovatich

no longer listed · 1.0.0

Leonid Kvecher

no longer listed · 1.0.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.0.3Latest
2025-01-09 · current release · diff ↗
1.0.2
2024-11-24 · diff ↗
1.0.1
2024-07-09 · diff ↗
1.0.0
2024-07-08
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-07-08
Total releases: 4 / 2 yrs
License: GPL (>= 3) OSI
Download size: 1.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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