Software

R

Downloads are from CRAN/Bioconductor/anaconda, updated on 2024-02-27.

Total downloads: 5.8M.

Visualization

Package Downloads GitHub Stars Publication
spiralize: Visualize data on spirals. CRAN GitHub stars
circlize: circular visualization in R. [#circlize on stackoverflow] CRAN GitHub stars
ComplexHeatmap: Flexibly arranging multiple heatmaps
    and self define annotation graphics.
Bioc GitHub stars
InteractiveComplexHeatmap: Makes interactive ComplexHeatmap. Bioc GitHub stars
EnrichedHeatmap: Visualizes the enrichment of genomic signals
    on specific target region.
Bioc GitHub stars
HilbertCurve: Making 2D Hilbert Curve. Bioc GitHub stars
gtrellis: genome-level trellis layout. Bioc GitHub stars
BioCartaImage: BioCarta pathway images. Bioc GitHub stars -

Data analysis

Package Downloads GitHub Stars Publication
simona: Semantic Similarity in Bio-Ontologies. Bioc GitHub stars -
simplifyEnrichment: Simplify functional enrichment results. Bioc GitHub stars
cola: A Framework for Consensus Partitioning. Bioc GitHub stars
rGREAT: Client of GREAT analysis. Bioc GitHub stars
CePa: centrality-based pathway enrichment. CRAN GitHub stars
YAPSA: Yet Another Package for Signature Analysis. (current maintainer) Bioc -

Data packages

Package Downloads GitHub Stars Publication
GeneSummary: RefSeq Gene Summaries. Bioc GitHub stars -
UniProtKeywords: Keywords from the UniProt database. Bioc GitHub stars -
BioMartGOGeneSets: Gene Ontology Gene Sets from BioMart. Bioc GitHub stars -

Teaching

Package Downloads GitHub Stars Publication
GSEAtraining: Learning gene set enrichment analysis. GitHub stars -

Other tools

Package Downloads GitHub Stars Publication
pkgndep: Check the Heaviness of Package Dependencies. CRAN GitHub stars
bsub: Submitter and monitor of LSF cluster. CRAN GitHub stars -
GetoptLong: wrapper of the Perl module Getopt::Long,
    also provides a simple variable interpolation in R.
CRAN GitHub stars -
GlobalOptions: setting global options in R. CRAN GitHub stars -

Perl

Package Downloads GitHub Stars Publication
rhydrogen: translate comments to documentations in R. - GitHub stars -
Microarray::GEO::SOFT: Reading microarray data in SOFT format from GEO database. - GitHub stars -
Statistics::Multtest: Control false discovery rate in multiple test problem. - GitHub stars -
List::Vectorize: functions to make vectorized calculation easy. - GitHub stars -
ngspipeline: NGS pipeline maker. - GitHub stars -

Books

Package status

Package GitHub Actions CRAN check bioc-devel bioc-release GitHub issues (opened) GitHub issues (closed)
circlize R-CMD-check - - GitHub issues GitHub issues
spiralize R-CMD-check - - GitHub issues GitHub issues
GetoptLong R-CMD-check - - GitHub issues GitHub issues
GlobalOptions R-CMD-check - - GitHub issues GitHub issues
bsub R-CMD-check - - GitHub issues GitHub issues
pkgndep R-CMD-check - - GitHub issues GitHub issues
YAPSA - - - -
simona R-CMD-check - GitHub issues GitHub issues
simplifyEnrichment R-CMD-check - GitHub issues GitHub issues
ComplexHeatmap R-CMD-check GitHub issues GitHub issues
InteractiveComplexHeatmap R-CMD-check - GitHub issues GitHub issues
EnrichedHeatmap R-CMD-check - GitHub issues GitHub issues
HilbertCurve R-CMD-check - GitHub issues GitHub issues
gtrellis R-CMD-check - GitHub issues GitHub issues
rGREAT R-CMD-check - GitHub issues GitHub issues
cola R-CMD-check - GitHub issues GitHub issues
GeneSummary R-CMD-check - - - GitHub issues GitHub issues
UniProtKeywords R-CMD-check - - - GitHub issues GitHub issues
BioMartGOGeneSets R-CMD-check - - - GitHub issues GitHub issues
BioCartaImage R-CMD-check - - - GitHub issues GitHub issues