R Observatory: Metrics for PSCBS version 0.68.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PSCBS

0.68.0

Analysis of Parent-Specific DNA Copy Numbers

3packages depend

12Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Henrik BengtssonFirst published 2011-06-1746 releasesCRAN page ↗GitHub ↗

Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.

Install

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

install.packages("PSCBS", 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("HenrikBengtsson/PSCBS")

Development version from HenrikBengtsson/PSCBS. 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-pscbs

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: 10.4 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.09

not tracked

Coverage

13

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

Documentation

READMEYes · 250 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 75%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 12%

Downloads

12K

CRAN downloads in the past year

Rank #4,064 · ~33/day · ~1K/mo

Releases R versions

Daily download trend is not available in this view yet.

55330 days

2K90 days

12K1 year

Compare downloads with other packages →

Also on289 r2u30.4K bioconda55 c2d4u

Repository

GitHub ↗ henrikbengtsson/pscbs

10Stars

4Forks

10Open issues

1Open PRs

0Releases

826Commits

4Contributors

rpackage

826 commits · Last activity 2025-04-18 · +11.1% stars, 30d

Stars over time

2025-08-19 · 82026-08-11 · 10

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/henrikbengtsson/pscbs on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Makefile

CRAN release process (1)

revdep/

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.2.0

Imports (13)

R.methodsS3 R.oo R.utils R.cache matrixStats aroma.light (>= 2.4.0)DNAcopy futureparallelgraphicsgrDevicesstatsutils

LinkingTo (0)

none

Suggests (3)

R.rsp R.devices ggplot2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

3indirect

aroma.cn aroma.core jointseg

Code & Tests

People & History

People (7)

Maintainer (1)

Henrik Bengtsson

Author, Maintainer, Copyright holder · added in 3.0.1

Authors (6)

Henrik Bengtsson

Author, Maintainer, Copyright holder · added in 3.0.1

Pierre Neuvial

Author · added in 3.0.1

Adam B. Olshen

Author · added in 3.0.1

Richard A. Olshen

Author · added in 3.0.1

Venkatraman E. Seshan

Author · added in 3.0.1

Paul T. Spellman

Author · added in 3.0.1

Contributors (1)

Frank E Harrell Jr

Contributor · added in 0.66.0

Copyright holders (1)

Henrik Bengtsson

Author, Maintainer, Copyright holder · added in 3.0.1

Listed in earlier versions (7)

H. Bengtsson