R Observatory: Metrics for mutSignatures version 2.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

mutSignatures

2.1.1Package record

Decipher Mutational Signatures from Somatic Mutational Catalogs

0packages depend

3.2Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Damiano FantiniCRAN page ↗Website ↗

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)Fedora (COPR)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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-mutSignatures

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-mutSignatures

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Damiano Fantini <damiano.fantini@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Damiano",
                      family = "Fantini",
                      role = c("aut", "cre"),
                      email = "damiano.fantini@gmail.com"),
               person(given = "Vania",
                      family = "Vidimar",
                      role = "aut"),
               person(given = c("Joshua", "J"),
                      family = "Meeks",
                      role = "aut"))
as necessary.

CRAN check page ↗

Slowest check: 2.7 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-06-09
ERROR11 OK, 1 NOTE, 1 ERROR2026-06-08
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.1.1

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileYes · computed when R runs itWebsiteYes

Help pages: 66 (13 internal)includes a package overview page
Examples that run: 100%25 run in a plain check
Exported functions with examples: 64%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 52%

Vignettes (1)

Getting Started with mutSignatures HTML

How these are measured

Downloads

3.2K

CRAN downloads in the past year

Rank #9,656 · ~9/day · ~269/mo

Releases R versions

Daily download trend is not available in this view yet.

37130 days

1K90 days

3.2K1 year

Compare downloads with other packages →

Also on110 r2u4 autocran51 c2d4u

How downloads are counted

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing mutSignatures adds 22 packages (8 with compiled code, 15 MB of source tarballs). Heaviest: ggplot2 6.0 MB, isoband 1.5 MB, farver 1.2 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (3)

Damiano Fantini

Vania Vidimar

· added in 2.0.1

Joshua J Meeks

Maintainer since 1.2 (2017)

Releases (3)

Pick two releases to compare their code metrics.

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
record
2020-11-09 · current release · diff ↗
2.0.1
record
2020-07-06 · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+

added 22 exports
attachContext, attachMutType, countMutTypes, decipherMutationalProcesses, extractXvarlinkData, filterSNV, frequencize, getCosmicSignatures, importVCFfiles, matchSignatures, plotMutTypeProfile, plotSignExposures, prelimProcessAssess, processVCFdata, removeMismatchMut, resolveMutSignatures, revCompl, setMutClusterParams, silhouetteMLB, simplifySignatures, sortByMutations, table2df
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
record
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
Minimum R: ≥ 3.5
Bundled data: 438 KB / 1 file
Download size: 921 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("mutSignatures")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 mutSignatures version 2.1.1 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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