mutSignatures

2.1.1

Decipher Mutational Signatures from Somatic Mutational Catalogs

0packages depend

3.3Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Damiano FantiniFirst published 2017-01-243 releasesCRAN page ↗

Cancer cells accumulate DNA mutations as result of DNA damage and DNA repair processes. This computational framework is aimed at deciphering DNA mutational signatures operating in cancer. The framework includes modules that support raw data import and processing, mutational signature extraction, and results interpretation and visualization. The framework accepts widely used file formats storing information about DNA variants, such as Variant Call Format files. The framework performs Non-Negative Matrix Factorization to extract mutational signatures explaining the observed set of DNA mutations. Bootstrapping is performed as part of the analysis. The framework supports parallelization and is optimized for use on multi-core systems. The software was described by Fantini D et al (2020) doi:10.1038/s41598-020-75062-0 and is based on a custom R-based implementation of the original MATLAB WTSI framework by Alexandrov LB et al (2013) doi:10.1016/j.celrep.2012.12.008.

Install

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

install.packages("mutSignatures", 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-mutsignatures

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

# 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-mutSignatures

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

Health

CRAN checks

2NOTE11OK

Failing flavors

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

Slowest check: 2.9 min · r-devel-linux-x86_64-fedora-clang

Check history

NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

Documentation signals are not tracked yet for this package.

Downloads

3.3K

CRAN downloads in the past year

Rank #13,471 · ~9/day · ~278/mo

mutSignatures Releases R versions

Daily download trend is not available in this view yet.

28430 days

78390 days

3.3K1 year

Compare downloads with other packages →

Also on115 r2u21 autocran32 c2d4u

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.5foreach

Imports (8)

graphicsstatsclusterdoParallel ggplot2 pracma proxymethods

LinkingTo (0)

none

Suggests (6)

dplyr reshape2 kableExtra gridExtra knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (3)

Damiano Fantini

no longer listed · 1.2 to 2.1.1

Joshua J Meeks

no longer listed · 1.2 to 2.1.1

Vania Vidimar

no longer listed · 2.0.1 to 2.1.1

Package Timeline

3 releases. 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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
2.1.1Latest
2020-11-09 · current release · diff ↗
2.0.1
2020-07-06 · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
1.2
2017-01-24
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-01-24
Total releases: 3 / 9 yrs
License: GPL-2 OSI
Download size: 921 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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