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https://github.com/shixiangwang/sigminer

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html
https://github.com/shixiangwang/sigminer

Keywords

bayesian-nmf bioinformatics cancer-research cnv copynumber-signatures cosmic-signatures dbs easy-to-use indel mutational-signatures nmf nmf-extraction r sbs signature-extraction somatic-mutations somatic-variants visualization

Keywords from Contributors

cancer-dataset shiny-apps ucsc-xena

Last synced: 11 months ago
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Repository metadata

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

Owner metadata

Committers metadata

Last synced: 12 months ago

Total Commits: 1,144
Total Committers: 8
Avg Commits per committer: 143.0
Development Distribution Score (DDS): 0.053

Commits in past year: 28
Committers in past year: 1
Avg Commits per committer in past year: 28.0
Development Distribution Score (DDS) in past year: 0.0

Name Email Commits
ShixiangWang w****x@s****n 1083
Shixiang Wang w****g@1****m 30
taoziyu97 b****i@s****m 16
lihm1 4****1 7
wutao 1****5@q****m 4
lihm1 l****m@s****n 2
Qi ZHAO z****i@s****n 1
selkamand s****d@g****m 1

Committer domains:

Issue and Pull Request metadata

Last synced: 12 months ago

Total issues: 99
Total pull requests: 18
Average time to close issues: about 1 month
Average time to close pull requests: about 23 hours
Total issue authors: 33
Total pull request authors: 5
Average comments per issue: 4.23
Average comments per pull request: 0.56
Merged pull request: 17
Bot issues: 0
Bot pull requests: 0

Past year issues: 17
Past year pull requests: 0
Past year average time to close issues: 10 days
Past year average time to close pull requests: N/A
Past year issue authors: 9
Past year pull request authors: 0
Past year average comments per issue: 3.65
Past year average comments per pull request: 0
Past year merged pull request: 0
Past year bot issues: 0
Past year bot pull requests: 0

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/shixiangwang/sigminer

Top Issue Authors

  • ShixiangWang (37)
  • xiw588 (12)
  • lincj1994 (6)
  • selkamand (4)
  • wangshun1121 (4)
  • RuimeiL (3)
  • rajeha (3)
  • joonan30 (3)
  • KirsieMin (2)
  • tangwei1129 (2)
  • toddajohnson (1)
  • Sonia-Bedi (1)
  • songeric1107 (1)
  • tucker-bower-psjh (1)
  • WiesVallentgoed (1)

Top Pull Request Authors

  • ShixiangWang (9)
  • taoziyu97 (4)
  • lihm1 (3)
  • selkamand (1)
  • likelet (1)

Top Issue Labels

  • enhancement (19)
  • bug (8)
  • good first issue (7)
  • question (5)
  • help wanted (3)
  • QA (3)
  • doc (3)
  • 存档 (1)
  • bioconda (1)

Top Pull Request Labels

Package metadata

cran.r-project.org: sigminer

Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

  • Homepage: https://github.com/ShixiangWang/sigminer
  • Documentation: http://cran.r-project.org/web/packages/sigminer/sigminer.pdf
  • Licenses: MIT + file LICENSE
  • Latest release: 2.3.1 (published 12 months ago)
  • Last Synced: 2024-05-14T21:42:23.909Z (12 months ago)
  • Versions: 34
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 841 Last month
  • Rankings:
    • Stargazers count: 3.348%
    • Forks count: 4.354%
    • Average: 15.422%
    • Downloads: 16.963%
    • Dependent repos count: 23.793%
    • Dependent packages count: 28.652%
  • Maintainers (1)

Dependencies

DESCRIPTION cran
  • R >= 3.5 depends
  • NMF * imports
  • Rcpp * imports
  • cli >= 2.0.0 imports
  • cowplot * imports
  • data.table * imports
  • dplyr * imports
  • furrr >= 0.2.0 imports
  • future * imports
  • ggplot2 >= 3.3.0 imports
  • ggpubr * imports
  • maftools * imports
  • magrittr * imports
  • methods * imports
  • purrr * imports
  • rlang >= 0.1.2 imports
  • stats * imports
  • tidyr * imports
  • BSgenome * suggests
  • BSgenome.Hsapiens.UCSC.hg19 * suggests
  • Biobase * suggests
  • Biostrings * suggests
  • GenSA * suggests
  • GenomicRanges * suggests
  • IRanges * suggests
  • R.utils * suggests
  • RColorBrewer * suggests
  • UCSCXenaTools * suggests
  • circlize * suggests
  • cluster * suggests
  • copynumber * suggests
  • covr * suggests
  • digest * suggests
  • ggalluvial * suggests
  • ggcorrplot * suggests
  • ggfittext * suggests
  • ggplotify * suggests
  • ggrepel * suggests
  • knitr * suggests
  • lpSolve * suggests
  • markdown * suggests
  • matrixStats * suggests
  • nnls * suggests
  • parallel * suggests
  • patchwork * suggests
  • pheatmap * suggests
  • quadprog * suggests
  • reticulate * suggests
  • rmarkdown * suggests
  • roxygen2 * suggests
  • scales * suggests
  • synchronicity * suggests
  • testthat * suggests
  • tibble * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite

Score: 13.736389425509817