R Observatory: Metrics for cosmicsig version 1.3.1

Balamuta, James Joseph

cosmicsig

1.3.1

Mutational Signatures from COSMIC (Catalogue of Somatic Mutations in Cancer)

1packages depend

3.9Kdownloads / year

66.7%test coverage

13/13checks pass

Overview

About

Maintained by Steven RozenFirst published 2021-12-203 releasesCRAN page ↗GitHub ↗

A data package with 2 main package variables: 'signature' and 'etiology'. The 'signature' variable contains the latest mutational signature profiles released on COSMIC https://cancer.sanger.ac.uk/signatures/ for 3 mutation types: * Single base substitutions in the context of preceding and following bases, * Doublet base substitutions, and * Small insertions and deletions. 'cosmicsig' stands for COSMIC signatures. Please run ?'cosmicsig' for more information.

Install

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

install.packages("cosmicsig", 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("Rozen-Lab/cosmicsig")

Development version from Rozen-Lab/cosmicsig. 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-cosmicsig

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-cosmicsig

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-cosmicsig

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

Health

CRAN checks

13OK

Slowest check: 59 s · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.05

66.7%

Coverage · measured lines

100%

Documentation · exports

0

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
OK2026-04-26
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
8 OK · 6 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 68 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

3.9K

CRAN downloads in the past year

Rank #6,038 · ~11/day · ~328/mo

Releases R versions

Daily download trend is not available in this view yet.

22930 days

1.4K90 days

3.9K1 year

Compare downloads with other packages →

Also on160 r2u3 autocran

Repository

GitHub ↗ rozen-lab/cosmicsig

1Stars

0Forks

0Open issues

0Open PRs

2Releases

95Commits

2Contributors

95 commits · Last activity 2026-04-22

Stars over time

2022-02-23 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/rozen-lab/cosmicsig on 2026-08-03.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

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

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: claude on 2026-04-19

claude

Most recent: claude on 2026-04-19

Evidence

claude: on 2026-04-19 · evidence B, D

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (0)

none

LinkingTo (0)

none

Suggests (2)

testthat usethis

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

mSigTools

Code & Tests

People & History

People (2)

Maintainer (1)

Steven Rozen

Author, Maintainer

Authors (2)

Steven Rozen

Author, Maintainer

Nanhai Jiang

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.3.1Latest
2026-04-21 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.1.1
2023-08-30 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.0.7
2021-12-20
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-12-20
Total releases: 3 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5
Bundled data: 2.6 MB / 8 files
Download size: 1.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Start here. This is the citation for the package itself.

citation("cosmicsig")

CRAN DOI

https://doi.org/10.32614/CRAN.package.cosmicsig

BibTeX, derived from DESCRIPTION

@Manual{cosmicsig,
  title  = {cosmicsig: Mutational Signatures from COSMIC (Catalogue of Somatic
Mutations in Cancer)},
  author = {Rozen, Steven and Jiang, Nanhai},
  year   = {2026},
  note   = {R package version 1.3.1},
  doi    = {10.32614/CRAN.package.cosmicsig},
  url    = {https://CRAN.R-project.org/package=cosmicsig}
}

Derived from the package DESCRIPTION, not from a citation file the authors wrote. If they publish one later, prefer it.

This is the citation for the package. It is not a citation for the R Observatory.

Cite this page

Use this when the claim is about a measurement on this page.

BibTeX

@misc{robservatorycosmicsig,
  author    = {Balamuta, James Joseph},
  title     = {{R} {Observatory}: Metrics for {cosmicsig} version 1.3.1},
  year      = {2026},
  publisher = {HJJB, LLC},
  url       = {https://r-observatory.thecoatlessprofessor.com/packages/cosmicsig},
  note      = {Data set. Data release v2026-08-05}
}

APA

Balamuta, J. J. (2026). R Observatory: Metrics for cosmicsig version 1.3.1 [Data set]. HJJB, LLC. Data release v2026-08-05. https://r-observatory.thecoatlessprofessor.com/packages/cosmicsig

RIS

TY  - DATA
AU  - Balamuta, James Joseph
TI  - R Observatory: Metrics for cosmicsig version 1.3.1
PY  - 2026
PB  - HJJB, LLC
N1  - Data release v2026-08-05
UR  - https://r-observatory.thecoatlessprofessor.com/packages/cosmicsig
ER  -

In prose

These package metrics were obtained from the R Observatory (Balamuta, 2026), data release v2026-08-05, https://r-observatory.thecoatlessprofessor.com/packages/cosmicsig.

Bound to data release v2026-08-05, which is what makes the numbers on this page reproducible. See how to cite.

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