sigminer

2.3.1

Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

0packages depend

7.1Kdownloads / year

–test coverage

0/13checks pass

Overview

About

Maintained by Shixiang WangFirst published 2019-04-2534 releasesCRAN page ↗GitHub ↗

Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2021) DOI:10.1371/journal.pgen.1009557 & Alexandrov, Ludmil B., et al. (2020) DOI:10.1038/s41586-020-1943-3 & Steele Christopher D., et al. (2022) DOI:10.1038/s41586-022-04738-6). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.

Install

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

install.packages("sigminer", 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("ShixiangWang/sigminer")

Development version from ShixiangWang/sigminer. 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-sigminer

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

13NOTE

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
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 7.4 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

99%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-06-09
0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-22
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
0 OK · 13 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 795 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 70%
Documented parameters: 97%
Return-value docs: 93%
References docs: 15%

Downloads

7.1K

CRAN downloads in the past year

Rank #6,417 · ~19/day · ~588/mo

Releases R versions

Daily download trend is not available in this view yet.

51430 days

1.6K90 days

7.1K1 year

Compare downloads with other packages →

Also on431 r2u5.6K bioconda

Repository

GitHub ↗ shixiangwang/sigminer

163Stars

20Forks

15Open issues

2Open PRs

35Releases

1,269Commits

8Contributors

mutational-signaturescopynumber-signaturessomatic-variantssomatic-mutationscosmic-signaturessignature-extractionnmfnmf-extraction

1,269 commits · Last activity 2025-12-25 · +0.6% stars, 30d

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/shixiangwang/sigminer on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

CRAN-SUBMISSION

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

49 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (17)

cli cowplot data.table dplyr furrr future ggplot2 ggpubr maftools magrittrmethodsNMF purrr Rcpp rlangstatstidyr

LinkingTo (1)

Rcpp

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 19,344 (74%)Rd 6,374 (24%)Vignettes 234 (1%)C++ 103 (0%)

Code characteristics

Object systems

S35S4 class2S4 method2

Cyclomatic complexity: 3.0 median / 66 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

265 102 exported

Complexity

5.5 avg / 66 max

Call network

265 nodes / 342 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

Datasets

Bundled datasets · 15

Name	Class	Rows × Cols	Also ships in
centromeres.T2T	data.frame	23 × 3	–
centromeres.hg19	data.frame	24 × 3	–
centromeres.hg38	data.frame	24 × 3	–
centromeres.mm10	data.frame	21 × 3	–
centromeres.mm9	data.frame	21 × 3	–
chromsize.T2T	data.frame	25 × 2	–
chromsize.hg19	data.frame	93 × 2	–
chromsize.hg38	data.frame	455 × 2	–
chromsize.mm10	data.frame	66 × 2	–
chromsize.mm9	data.frame	35 × 2	–
cytobands.T2T	data.frame	862 × 5	–
cytobands.hg19	data.frame	862 × 5	–
cytobands.hg38	data.frame	862 × 5	–
cytobands.mm10	data.frame	403 × 5	–
cytobands.mm9	data.frame	403 × 5	–

People & History

People (6)

Maintainer (1)

Shixiang Wang

Author, Maintainer

Authors (5)

Shixiang Wang

Author, Maintainer

Huimin Li

Author · added in 1.2.1

Xue-Song Liu

Author, Contributor

Ziyu Tao

Author · added in 1.0.3

Tao Wu

Author · added in 1.0.3

Contributors (2)

Xue-Song Liu

Author, Contributor

Anand Mayakonda

Contributor · added in 1.0.0

Listed in earlier versions (1)

Geoffrey Macintyre

no longer listed · 0.1.9 to 1.2.5

Package Timeline

34 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
2.3.1Latest
2024-05-11 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
2.3.0
2023-12-12 · diff ↗
2.2.2
2023-08-21 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.2.0
2023-04-06 · diff ↗
2.1.9
2022-11-09 · diff ↗
2.1.8
2022-10-20 · diff ↗
2.1.7
2022-08-31 · diff ↗
2.1.6
2022-08-09 · diff ↗
2.1.5
2022-06-30 · diff ↗
2.1.4
2022-04-26 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.1.3
2022-03-10 · diff ↗

Show 27 earlier events

2.1.2
2021-12-15 · diff ↗
2.1.1
2021-10-29 · diff ↗
2.1.0
2021-09-22 · diff ↗
2.0.5
2021-09-03 · diff ↗
2.0.4
2021-08-03 · diff ↗
2.0.3
2021-07-19 · diff ↗
2.0.2
2021-06-17 · diff ↗
2.0.1
2021-05-19 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.0.0
2021-04-01 · diff ↗
1.2.5
2021-02-20 · diff ↗
1.2.4
2021-01-31 · diff ↗
1.2.1
2021-01-08 · diff ↗
1.1.0
2020-11-11 · diff ↗
1.0.19
2020-09-28 · diff ↗
1.0.16
2020-09-12 · diff ↗
1.0.13
2020-08-27 · diff ↗
1.0.7
2020-06-17 · diff ↗
1.0.6
2020-06-01 · diff ↗
1.0.5
2020-05-14 · diff ↗
1.0.3
2020-05-01 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.0
2020-03-31 · diff ↗
0.1.11
2019-05-07 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.1.9
2019-04-25
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-04-25
Total releases: 34 / 7 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5
Bundled data: 789 KB / 22 files
Download size: 4.0 MB
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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