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Open Source Science

https://github.com/bhklab/toxicogx

A statistical package, in R, used in cancer research to analyze toxicity of drugs on cancer gene expression across large-scale toxicogenomic datasets.

https://github.com/bhklab/toxicogx

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 11 committers (9.1%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.9%) to scientific vocabulary

Keywords from Contributors

pharmacogx pharmacogenomic gene transcriptomics ontology bioconductor-package proteomics grna-sequence genomics sequencing
Last synced: 11 months ago · JSON representation

Repository

A statistical package, in R, used in cancer research to analyze toxicity of drugs on cancer gene expression across large-scale toxicogenomic datasets.

Basic Info
  • Host: GitHub
  • Owner: bhklab
  • License: other
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 81.7 MB
Statistics
  • Stars: 6
  • Watchers: 5
  • Forks: 3
  • Open Issues: 0
  • Releases: 0
Created about 7 years ago · Last pushed over 3 years ago
Metadata Files
Readme Changelog License

README.md

R build status

Bioc-Release: Bioconductor RELEASE Bioc-Devel: Bioconductor DEVEL

ToxicoGx

A statistical analysis package for use exploring the relationship between toxicity and gene expression in specific cell types. The package includes a specialized object, the ToxicoSet, which allows unified storage of all data related to a specific toxico-genomic study. Methods accepting this object are inlcuded for summarize results and annotaiton, conduct various analyses as well as to visualize the results thereof.

Owner

  • Name: BHKLAB
  • Login: bhklab
  • Kind: organization
  • Location: Toronto, Ontario, Canada

The Haibe-Kains Laboratory @ Princess Margaret Cancer Centre

GitHub Events

Total
Last Year

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 427
  • Total Committers: 11
  • Avg Commits per committer: 38.818
  • Development Distribution Score (DDS): 0.468
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
ChristopherEeles c****s@o****m 227
Esther y****0@g****m 67
cjtangyx 5****x 40
Amy Tang a****g@g****m 40
sisiranair 4****r 33
Nitesh Turaga n****a@g****m 8
Jermiah BHK j****8@g****m 5
mnakano m****o@g****m 2
Petr Smirnov p****0@g****m 2
J Wokaty j****y@s****u 2
chris_eeles y****u@e****m 1
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 1
  • Total pull requests: 8
  • Average time to close issues: 5 minutes
  • Average time to close pull requests: about 1 hour
  • Total issue authors: 1
  • Total pull request authors: 3
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • hpages (1)
Pull Request Authors
  • ChristopherEeles (6)
  • p-smirnov (1)
  • ParwaizN (1)
Top Labels
Issue Labels
Pull Request Labels
bug (2)

Dependencies

DESCRIPTION cran
  • CoreGx * depends
  • R >= 4.1 depends
  • Biobase * imports
  • BiocGenerics * imports
  • BiocParallel * imports
  • S4Vectors * imports
  • SummarizedExperiment * imports
  • assertthat * imports
  • caTools * imports
  • data.table * imports
  • downloader * imports
  • dplyr * imports
  • ggplot2 * imports
  • grDevices * imports
  • graphics * imports
  • jsonlite * imports
  • limma * imports
  • magrittr * imports
  • methods * imports
  • parallel * imports
  • reshape2 * imports
  • scales * imports
  • stats * imports
  • tibble * imports
  • tidyr * imports
  • utils * imports
  • BiocStyle * suggests
  • PharmacoGx * suggests
  • devtools * suggests
  • knitr * suggests
  • markdown * suggests
  • rmarkdown * suggests
  • testthat * suggests
  • tinytex * suggests
  • xtable * suggests
.github/workflows/R-CMD-check-bioc-release.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact v2 composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/R-CMD-check-bioc.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact v2 composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action 4.1.4 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite