Data

Tools

Indexes

Applications

Experiments

Open Source Science

pharmacogx

R package to analyze large-scale pharmacogenomic datasets.

https://github.com/bhklab/pharmacogx

Science Score: 36.0%

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
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    4 of 25 committers (16.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (3.8%) to scientific vocabulary

Keywords

datasets pharmacogenomic pharmacogx

Keywords from Contributors

bioconductor-package genomics gene transcriptomics bioconductor metabolomics bioinformatics mass-spectrometry core-package single-cell
Last synced: 6 months ago · JSON representation

Repository

R package to analyze large-scale pharmacogenomic datasets.

Basic Info
Statistics
  • Stars: 70
  • Watchers: 24
  • Forks: 26
  • Open Issues: 75
  • Releases: 0
Topics
datasets pharmacogenomic pharmacogx
Created over 10 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct

README.md

PharmacoGx

==========

R build status

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

R package to analyze large-scale pharmacogenomic datasets.

Installation

R if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("PharmacoGx")

Development version

R if (!requireNamespace("pak", quietly = TRUE)) install.packages("pak") pak::pkg_install("bhklab/PharmacoGx")

Owner

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

The Haibe-Kains Laboratory @ Princess Margaret Cancer Centre

GitHub Events

Total
  • Issues event: 10
  • Watch event: 4
  • Member event: 1
  • Issue comment event: 9
  • Push event: 26
  • Pull request event: 1
  • Create event: 3
Last Year
  • Issues event: 10
  • Watch event: 4
  • Member event: 1
  • Issue comment event: 9
  • Push event: 26
  • Pull request event: 1
  • Create event: 3

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 952
  • Total Committers: 25
  • Avg Commits per committer: 38.08
  • Development Distribution Score (DDS): 0.574
Past Year
  • Commits: 36
  • Committers: 3
  • Avg Commits per committer: 12.0
  • Development Distribution Score (DDS): 0.111
Top Committers
Name Email Commits
ChristopherEeles c****s@o****m 406
Petr Smirnov p****0@g****m 309
Jermiah j****8@g****m 58
Petr Smirnov p****v@s****a 43
Benjamin Haibe-Kains b****s@u****a 35
ff98li l****l@g****m 15
Nitesh Turaga n****a@g****m 14
b.haibe-kains b****s@b****8 14
J Wokaty j****y@s****u 10
markcfreeman m****n@g****m 10
Jermiah j****h@g****m 9
zhaleh-safikhani z****i@g****m 5
Herve Pages h****s@f****g 4
mnakano m****o@g****m 3
Hervé Pagès h****s@f****g 2
Robert Allaway a****y 2
vobencha v****a@g****m 2
vobencha v****n@r****g 2
hpages@fhcrc.org h****s@f****g@b****8 2
A Wokaty a****y@s****u 2
mzon7 m****7@g****m 1
Martin Morgan m****n@f****g 1
mtmorgan@fhcrc.org m****n@f****g@b****8 1
lshep l****d@r****g 1
LiNk-NY m****9@g****m 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 4 roswellpark.org: 2 sph.cuny.edu: 2 fredhutch.org: 1 utoronto.ca: 1 sri.utoronto.ca: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 97
  • Total pull requests: 13
  • Average time to close issues: 8 months
  • Average time to close pull requests: 2 days
  • Total issue authors: 46
  • Total pull request authors: 6
  • Average comments per issue: 2.08
  • Average comments per pull request: 0.62
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 6
  • Pull requests: 1
  • Average time to close issues: 15 days
  • Average time to close pull requests: about 20 hours
  • Issue authors: 4
  • Pull request authors: 1
  • Average comments per issue: 0.83
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • bhaibeka (17)
  • p-smirnov (14)
  • MomenehForoutan (7)
  • jjjermiah (5)
  • spocks (3)
  • markcfreeman (3)
  • soheilj (3)
  • OrysyaStus (3)
  • KatynaSada (2)
  • ChristopherEeles (2)
  • alimadani (2)
  • kkmkoudijs (2)
  • FarzanT (2)
  • khughitt (2)
  • DGendoo (2)
Pull Request Authors
  • p-smirnov (5)
  • ChristopherEeles (4)
  • jjjermiah (4)
  • mtran-code (1)
  • allaway (1)
  • kkmkoudijs (1)
  • raymond126 (1)
  • mzon7 (1)
Top Labels
Issue Labels
enhancement (9) bug (9) question (2)
Pull Request Labels
enhancement (1)

Dependencies

DESCRIPTION cran
  • CoreGx * depends
  • R >= 3.6 depends
  • Biobase * imports
  • BiocGenerics * imports
  • BiocParallel * imports
  • MultiAssayExperiment * imports
  • RColorBrewer * imports
  • S4Vectors * imports
  • SummarizedExperiment * imports
  • boot * imports
  • caTools * imports
  • checkmate * imports
  • coop * imports
  • data.table * imports
  • downloader * imports
  • ggplot2 * imports
  • grDevices * imports
  • graphics * imports
  • jsonlite * imports
  • magicaxis * imports
  • methods * imports
  • parallel * imports
  • reshape2 * imports
  • stats * imports
  • utils * imports
  • BiocStyle * suggests
  • crayon * suggests
  • knitcitations * suggests
  • knitr * suggests
  • markdown * suggests
  • pander * suggests
  • rmarkdown * suggests
  • testthat * suggests
.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
.github/workflows/R-CMD-check-bioc-release.yml.deprecated actions
.github/workflows/R-CMD-check-bioc.yml.deprecated actions
  • actions/cache v4 composite
  • actions/checkout v2 composite
  • actions/upload-artifact v4 composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/check-bioc.yml actions
  • JamesIves/github-pages-deploy-action releases/v4 composite
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v4 composite
  • docker/login-action v2 composite
  • docker/setup-buildx-action v2 composite
  • docker/setup-qemu-action v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
Dockerfile docker
  • ${BASE_IMAGE} latest build