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sigminer

2.4.0Package record

Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

0packages depend
8.2Kdownloads / year
–test coverage
13/13flavors OK

Overview

About
Maintained by Shixiang WangCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 2.4.0
  • sig_extract(), sig_estimate() and bp_extract_signatures() gained a backend = c("R", "rust") argument (issue #478, parity plan P1). "R" keeps the in-package **NMF** engine byte-for-byte; "rust" routes the decomposition across an isolated process boundary to the certified in-house Apache-2.0 KL-MU kernel shipped with the msuiter package (optional, runtime-gated; install from https://github.com/WangLabCSU/msuiter — not yet on CRAN): msuiter-kernel fit-kl, protocol 1, with a frozen --version handshake, fail-closed output parsing, a fixed iteration budget via option sigminer.rust_iters (default 2000) and an explicit per-run seed law (seed + i - 1 for run i of nrun). The rust path is mutually exclusive with pynmf = TRUE and expects a KL-family method ("brunet").
  • Fixed the SigProfiler interop recall command (sigprofiler_extract() fallback path after the reticulate call fails) to escape Windows backslash paths before embedding them in the Python -c payload (issue #470): literal backslashes are doubled for the cmd.exe layer, and values that can not travel the shell + python layers safely (embedded quotes, line breaks, %VAR% expansion, POSIX backslashes, $/backtick expansion, word-splitting whitespace in the Python path) are now rejected with an actionable error instead of emitting a broken command.
Show all changes in 2.4.0Hide the rest of the changes in 2.4.0
  • sigprofiler_extract(output_matrix_only = TRUE) no longer requires the Python / reticulate / conda stack: the matrix-file hand-off is pure R.
  • Clarified the sigprofiler_import(type = "refit") documentation against the current SigProfilerExtractor output tree: the branch reads Suggested_Solution/COSMIC_<MT>_Decomposed_Solution, which current versions emit unconditionally; the upstream option that was removed is refit_denovo_signatures on the extract side. The refit import branch stays functional and is now pinned by fixture tests.
  • Added testthat fixture round-trip coverage for the interop bridge and a local-only SigProfilerExtractor version-matrix harness (opt-in via SIGMINER_SP_MATRIX=1; deliberately not wired into CI, see tests/testthat/README-sigprofiler-matrix.md).
  • sig_fit() gained two opt-in likelihood-based refit methods (parity plan P3): method = "likelihood", a clean-room implementation of the MuSiCal bidirectional stepwise selection under the multinomial likelihood (Jin et al., Nature Genetics 56:541-552, 2024; see ?sig_fit references), with the acceptance thresholds exposed as the caller-overridable ll_add / ll_keep arguments — the paper describes them as study-optimized parameters, and the in-lane defaults (8 / 8) are a fixture calibration, not paper constants; and method = "lrt", a clean-room implementation of the PASA likelihood-ratio presence tests with the stop and minimality criteria at the significance level alpha (Jiang et al., Briefings in Bioinformatics 26(1):bbaf042, 2025; default alpha = 0.01, in-lane calibration). Both methods refit the selected set with the same QP simplex engine that drives method = "QP", reject auto_reduce (their decision layer already selects the reference set), and are also available on the bootstrap surfaces sig_fit_bootstrap() and sig_fit_bootstrap_batch(). The legacy methods and the default remain unchanged.

From NEWS.md in the release

Install

Health

CRAN checks
13OK
Slowest check: 7.6 min · r-release-macos-x86_64
Status changes
  • OK13 OK2026-10-04
  • NOTE13 NOTE2026-06-09
  • ERROR12 NOTE, 1 ERROR2026-06-07
  • NOTE14 NOTE2026-04-22
  • ERROR13 NOTE, 1 ERROR2026-04-18
Show 1 earlier changeHide 1 earlier change
  • NOTE14 NOTE2026-03-10
Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.4.0
READMEYes · 872 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 2.4.0Citation fileYes · cites a publicationWebsiteYes · pkgdown
Help pages
108 (3 internal)includes a package overview page
Examples that run
70%57 run in a plain check · 23 only when donttest examples are enabled (R CMD check --as-cran) · 1 never run
Exported functions with examples
70%
Documented parameters
97%
Return-value docs
93%
Help pages citing references
15%
Vignettes (2)
How these are measured

Downloads

8.2K
CRAN downloads in the past year
Rank #3,207 · ~23/day · ~687/mo
Daily download trend is not available in this view yet.
2.4K30 days
3.7K90 days
8.2K1 year
Compare downloads with other packages →
Also on487 r2u6K bioconda
How downloads are counted

Repository

shixiangwang/sigminer ↗Account: ShixiangWang
162Stars
20Forks
7Open issues
0Open PRs
36Releases
1,298Commits
8Commit identities
mutational-signaturescopynumber-signaturessomatic-variantssomatic-mutationscosmic-signaturessignature-extractionnmfnmf-extraction
1,298 commits · Last activity 2026-10-21 · -0.6% stars, 30d · Discussions: 12 posts
Responsiveness
How these are sampled
PRs merged (all time)
97%
Median days to close, 50 most recently updated closed issues
6
Median days to close, 50 most recently updated closed PRs
0

Stars over time

2026-07-11 · 1622026-10-21 · 162
How these are measured
PracticesBeta

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

Checks run against github.com/shixiangwang/sigminer on 2026-10-21.

Continuous integration (2)
GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)
README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-21 · The repository has a site deploy workflow

pkgdown site last built 2026-10-21

Coverage (1)
Coverage reporting (Codecov)
Reproducibility and dev environment (1)
data-raw/
Show all practicesHide 2 practices
CRAN release process (2)
cran-comments.mdCRAN-SUBMISSION
Lint, format, editor (1)
RStudio project
How this is detected·Detection ruleset v4 (2026-10-20)
AI coding toolsBeta

This repository shows signs of AI coding tools.

  • GitHub Copilotfirst seen 2025-12-25
    Pull request: opened by its own account
    Commits: 8 by its own account
  • Claude Codefirst seen 2026-10-14
    Pull request it wrote: opened by a project member
    Commits: at least 1 crediting it in the message
Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies
51 external dependencies (excludes base and recommended)

Installing sigminer adds 85 packages (39 with compiled code, 76 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 2 more not on CRAN are not measured.

Depends (1)
R >= 3.5
Imports (18)
clicowplotdata.tabledplyrfurrrfutureggplot2ggpubrmaftoolsmagrittrmethodsNMFparallellypurrrRcpprlangstatstidyr
LinkingTo (1)
Rcpp
Suggests (36)
BiobaseBiostringsBSgenomeBSgenome.Hsapiens.UCSC.hg19circlizeclustercovrdigestdoParallelGenomicRangesGenSAggalluvialggcorrplotggfittextggplotifyggrepelIRangesknitrlpSolvemarkdownmatrixStatsnnlsparallelpatchworkpheatmapquadprogR.utilsRColorBrewerreticulatermarkdownroxygen2scalessynchronicitytestthattibbleUCSCXenaTools
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 (6)
Shixiang Wang ORCID iD
Author, Maintainer since 0.1.9 (2019)
Huimin Li ORCID iD
Author · added in 1.2.1
Xue-Song Liu ORCID iD
Author, Contributor
Ziyu Tao ORCID iD
Author · added in 1.0.3
Tao Wu ORCID iD
Author · added in 1.0.3
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
Releases (36)

Pick two releases to compare their code metrics.

Show 29 earlier eventsHide 29 earlier events
  • R
    R 4.2.0 released · 2022-04-22
  • 2.1.3
    record
    2022-03-10 · diff ↗
  • 2.1.2
    record
    2021-12-15 · diff ↗
  • 2.1.1
    record
    2021-10-29 · diff ↗
  • 2.1.0
    record
    2021-09-22 · diff ↗ ·
    added 1 export
    sig_unify_extract
  • 2.0.5
    record
    2021-09-03 · diff ↗ ·
    added 3 exports
    get_intersect_size, get_pLOH_score, read_copynumber_ascat
  • 2.0.4
    record
    2021-08-03 · diff ↗ ·
    added 1 export
    get_Aneuploidy_score
  • 2.0.3
    record
    2021-07-19 · diff ↗
  • 2.0.2
    record
    2021-06-17 · diff ↗
  • 2.0.1
    record
    2021-05-19 · diff ↗
  • R
    R 4.1.0 released · 2021-05-18
  • 2.0.0
    record
    2021-04-01 · diff ↗ ·
    removed 1 export
    get_tidy_parameter
  • 1.2.5
    record
    2021-02-20 · diff ↗ ·
    added 1 export
    read_sv_as_rs
  • 1.2.4
    record
    2021-01-31 · diff ↗ ·
    added 2 exports
    bp_get_clustered_sigs, get_shannon_diversity_index
  • 1.2.1
    record
    2021-01-08 · diff ↗ ·
    added 12 exports
    bp_attribute_activity, bp_cluster_iter_list, bp_extract_signatures, bp_extract_signatures_iter, bp_get_rank_score, bp_get_sig_obj, bp_get_stats, bp_show_survey, bp_show_survey2, get_sig_rec_similarity, read_xena_variants, simulate_catalogue_matrix
  • 1.1.0
    record
    2020-11-11 · diff ↗ ·
    added 6 exports
    group_enrichment, same_size_clustering, show_cosmic, show_group_enrichment, simulate_catalogue, simulate_signature
  • 1.0.19
    record
    2020-09-28 · diff ↗ ·
    added 1 export
    show_cor
  • 1.0.16
    record
    2020-09-12 · diff ↗ ·
    added 6 exports
    get_sig_cancer_type_index, output_bootstrap, output_fit, output_sig, output_tally, show_group_distribution
  • 1.0.13
    record
    2020-08-27 · diff ↗ ·
    added 12 exports
    cosine, get_cn_freq_table, get_sig_db, read_copynumber_seqz, read_vcf, show_cn_freq_circos, show_cn_group_profile, show_sig_profile_heatmap, show_sig_profile_loop, sigprofiler_extract, sigprofiler_import, transform_seg_table
  • 1.0.7
    record
    2020-06-17 · diff ↗
  • 1.0.6
    record
    2020-06-01 · diff ↗ ·
    added 1 export
    show_groups
  • 1.0.5
    record
    2020-05-14 · diff ↗ ·
    added 6 exports
    .env, show_sig_bootstrap_error, show_sig_bootstrap_exposure, show_sig_bootstrap_stability, show_sig_fit, sig_fit_bootstrap_batch
  • 1.0.3
    record
    2020-05-01 · diff ↗ ·
    added 3 exports
    enrich_component_strand_bias, report_bootstrap_p_value, sig_fit_bootstrap
  • R
    R 4.0.0 released · 2020-04-24
  • 1.0.0
    record
    2020-03-31 · diff ↗ ·
    removed 24 exports
    GenomicVariation, draw_cn_components, draw_cn_distribution, draw_cn_features, draw_sig_activity, draw_sig_corrplot, draw_sig_profile, draw_subtypes_comparison, get_ArmLocation, get_LengthFraction, get_cnlist, get_cnsummary_sample, get_components, get_features, get_matrix, prepare_copynumber, read_variation, sig_assign_samples, sig_get_activity, sig_get_correlation, sig_get_similarity, sig_prepare, sig_summarize_subtypes, test_run_components
    added 50 exports
    :=, .data, add_h_arrow, add_labels, as_label, as_name, enquo, enquos, expr, get_adj_p, get_bayesian_result, get_cn_ploidy, get_genome_annotation, get_group_comparison, get_groups, get_sig_exposure, get_sig_feature_association, get_sig_similarity, get_tidy_association, get_tidy_parameter, handle_hyper_mutation, scoring, show_catalogue, show_cn_circos, show_cn_components, show_cn_distribution, show_cn_features, show_cn_profile, show_cosmic_sig_profile, show_group_comparison and 20 more
  • 0.1.11
    record
    2019-05-07 · diff ↗
  • R
    R 3.6.0 released · 2019-04-26
  • 0.1.9
    record
    2019-04-25
  • R
    R 3.5.0 released · 2018-04-23

Package metadata

First published
2019-04-25
Total releases
36 / 7 yrs
License
MIT + file LICENSE OSI
Minimum R
≥ 3.5
Bundled data
789 KB / 22 files
Download size
4.2 MB
Appears in task views
Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("sigminer")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1371/journal.pgen.1009557.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

APA

Balamuta, J. J. (2026). R Observatory: Metrics for sigminer version 2.4.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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