mSigTools

1.0.7

Mutational Signature Analysis Tools

0packages depend

2.4Kdownloads / year

95.0%test coverage

8/13checks pass

Overview

About

Maintained by Steven RozenFirst published 2022-08-302 releasesCRAN page ↗GitHub ↗

Utility functions for mutational signature analysis as described in Alexandrov, L. B. (2020) doi:10.1038/s41586-020-1943-3. This package provides two groups of functions. One is for dealing with mutational signature "exposures" (i.e. the counts of mutations in a sample that are due to each mutational signature). The other group of functions is for matching or comparing sets of mutational signatures. 'mSigTools' stands for mutational Signature analysis Tools.

Install

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

install.packages("mSigTools", 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/mSigTools")

Development version from Rozen-Lab/mSigTools. 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-msigtools

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-mSigTools

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-mSigTools

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

Health

CRAN checks

5NOTE8OK

Failing flavors

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

Slowest check: 1.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.85

95.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 56 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 90%
Return-value docs: 100%
References docs: 0%

Downloads

2.4K

CRAN downloads in the past year

Rank #20,053 · ~6/day · ~197/mo

Releases R versions

Daily download trend is not available in this view yet.

14030 days

55290 days

2.4K1 year

Compare downloads with other packages →

Also on97 r2u6 autocran

Repository

GitHub ↗ rozen-lab/msigtools

2Stars

2Forks

0Open issues

0Open PRs

3Releases

59Commits

2Contributors

License GPL-3.0 · 59 commits · Last activity 2025-06-30

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/rozen-lab/msigtools on 2026-08-02.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (4)

clue philentropy quadprog sets

LinkingTo (0)

none

Suggests (4)

cosmicsig ICAMS spelling testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Steven Rozen

Author, Maintainer

Authors (2)

Steven Rozen

Author, Maintainer

Nanhai Jiang

Author

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
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.0.7Latest
2023-01-13 · current release · diff ↗
1.0.5
2022-08-30
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-08-30
Total releases: 2 / 4 yrs
License: GPL-3 OSI
Download size: 35 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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