R Observatory: Metrics for PINSPlus version 2.0.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PINSPlus

2.0.9

Clustering Algorithm for Data Integration and Disease Subtyping

1packages depend

5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Van-Dung PhamFirst published 2018-03-1613 releasesCRAN page ↗

Provides a robust approach for omics data integration and disease subtyping. PINSPlus is fast and supports the analysis of large datasets with hundreds of thousands of samples and features. The software automatically determines the optimal number of clusters and then partitions the samples in a way such that the results are robust against noise and data perturbation (Nguyen et al. (2019) <DOI: 10.1093/bioinformatics/bty1049>, Nguyen et al. (2017)<DOI: 10.1101/gr.215129.116>, Nguyen et al. (2021)<DOI: 10.3389/fonc.2021.725133>).

Install

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

install.packages("PINSPlus", 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-pinsplus

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-PINSPlus

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-PINSPlus

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

Health

CRAN checks

13OK

Slowest check: 3.4 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

11

Dependencies · direct

Check history

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
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

5K

CRAN downloads in the past year

Rank #6,831 · ~14/day · ~417/mo

Releases R versions

Daily download trend is not available in this view yet.

33530 days

1.2K90 days

5K1 year

Compare downloads with other packages →

Also on427 r2u14 autocran28 c2d4u

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (11)

foreach entropy doParallel matrixStats Rcpp RcppParallel FNNclusterirlba mclust impute

LinkingTo (3)

Rcpp RcppArmadillo RcppParallel

Suggests (4)

knitr rmarkdownsurvivalmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

scISR

Code & Tests

People & History

People (5)

Maintainer (1)

Van-Dung Pham

Maintainer · added in 2.0.9

Authors (4)

Hung Nguyen

Author

Tin Nguyen

Author

Bang Tran

Author · added in 2.0.1

Duc Tran

Author · added in 2.0.1

Listed in earlier versions (1)

Sangam Shrestha

no longer listed · 1.0.0 to 2.0.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
2.0.9Latest
2025-07-29 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.0.7
2024-04-05 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
2.0.6
2021-12-14 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.0.5
2020-08-06 · diff ↗
2.0.4
2020-05-31 · diff ↗
2.0.3
2020-05-28 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.0.2
2020-04-13 · diff ↗
2.0.1
2020-04-02 · diff ↗
2.0.0
2019-06-04 · diff ↗

Show 7 earlier events

R
R 3.6.0 released · 2019-04-26
1.0.3
2019-01-07 · diff ↗
1.0.2
2018-07-17 · diff ↗
1.0.1
2018-05-03 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.0
2018-03-16
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-03-16
Total releases: 13 / 8 yrs
License: LGPL
Minimum R: ≥ 2.10
Bundled data: 594 KB / 3 files
Download size: 743 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PINSPlus")

Format

Pham, V., Nguyen, H., Nguyen, T., Tran, B., & Tran, D. (2025). PINSPlus: Clustering Algorithm for Data Integration and Disease Subtyping (Version 2.0.9) [Computer software]. https://doi.org/10.32614/CRAN.package.PINSPlus

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 PINSPlus version 2.0.9 [Data set]. HJJB, LLC. Data release v2026-08-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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