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compcodeR

https://github.com/csoneson/compcoder

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
    2 of 14 committers (14.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.5%) to scientific vocabulary

Keywords from Contributors

bioconductor-package bioconductor bioinformatics proteomics mass-spectrometry core-package feature-detection rnaseq peak-detection metabolomics
Last synced: 10 months ago · JSON representation

Repository

Basic Info
Statistics
  • Stars: 12
  • Watchers: 3
  • Forks: 4
  • Open Issues: 0
  • Releases: 0
Created about 12 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog

README.md

compcodeR

R build status

compcodeR is an R package that provides extensive functionality for comparing results obtained by different methods for differential expression analysis of (mainly) RNAseq data. It also contains functions for simulating count data and interfaces to several packages for performing the differential expression analysis.

The release version of compcodeR can be installed via Bioconductor:

install.packages("BiocManager") BiocManager::install("compcodeR")

The most recent (development) version can also be installed from GitHub directly:

BiocManager::install("csoneson/compcodeR")

Owner

  • Name: Charlotte Soneson
  • Login: csoneson
  • Kind: user

GitHub Events

Total
  • Watch event: 2
  • Push event: 6
  • Create event: 2
Last Year
  • Watch event: 2
  • Push event: 6
  • Create event: 2

Committers

Last synced: 12 months ago

All Time
  • Total Commits: 302
  • Total Committers: 14
  • Avg Commits per committer: 21.571
  • Development Distribution Score (DDS): 0.576
Past Year
  • Commits: 5
  • Committers: 3
  • Avg Commits per committer: 1.667
  • Development Distribution Score (DDS): 0.6
Top Committers
Name Email Commits
Charlotte Soneson c****n@g****m 128
Paul Bastide p****e@g****m 122
Nitesh Turaga n****a@g****m 14
J Wokaty j****y@s****u 10
d.tenenbaum d****m@b****8 8
Herve Pages h****s@f****g 5
Dan Tenenbaum d****a@f****g 4
vobencha v****a@g****m 2
Hervé Pagès h****s@f****g 2
vobencha v****n@r****g 2
A Wokaty a****y@s****u 2
roryk r****r@g****m 1
Kayla-Morrell k****l@r****g 1
Marc Carlson m****n@f****g 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 3 roswellpark.org: 2 sph.cuny.edu: 2 fredhutch.org: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 7
  • Total pull requests: 13
  • Average time to close issues: 21 days
  • Average time to close pull requests: 4 days
  • Total issue authors: 6
  • Total pull request authors: 3
  • Average comments per issue: 3.14
  • Average comments per pull request: 0.62
  • Merged pull requests: 13
  • 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
  • Ismail-Curie (2)
  • verasiwei (1)
  • 411an13 (1)
  • libcell (1)
  • hl-xue (1)
  • dsrobertson (1)
Pull Request Authors
  • pbastide (7)
  • csoneson (5)
  • roryk (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 27,209 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: compcodeR

RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 27,209 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 13.4%
Downloads: 40.2%
Maintainers (1)
charlottesoneson@gmail.com
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • sm * depends
  • DSS * enhances
  • rpanel * enhances
  • KernSmooth * imports
  • MASS * imports
  • ROCR * imports
  • ape * imports
  • caTools * imports
  • edgeR * imports
  • ggplot2 * imports
  • gplots * imports
  • grDevices * imports
  • graphics * imports
  • grid * imports
  • gtools * imports
  • knitr >= 1.2 imports
  • lattice >= 0.16 imports
  • limma * imports
  • markdown * imports
  • matrixStats * imports
  • methods * imports
  • modeest * imports
  • phylolm * imports
  • stats * imports
  • stringr * imports
  • tcltk * imports
  • utils * imports
  • vioplot * imports
  • BiocStyle * suggests
  • DESeq2 >= 1.1.31 suggests
  • EBSeq * suggests
  • NBPSeq >= 0.3.0 suggests
  • NOISeq * suggests
  • TCC * suggests
  • baySeq >= 2.2.0 suggests
  • covr * suggests
  • genefilter * suggests
  • ggtree * suggests
  • phangorn * suggests
  • phytools * suggests
  • rmarkdown * suggests
  • statmod * suggests
  • testthat * suggests
  • tidytree * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/cache v1 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • grimbough/bioc-actions/build-install-check v1 composite
  • grimbough/bioc-actions/run-BiocCheck v1 composite
  • grimbough/bioc-actions/setup-bioc v1 composite
  • r-lib/actions/setup-pandoc v2 composite