R
Downloads are from CRAN/Bioconductor/anaconda, updated on 2025-03-25.
Total downloads: 7.5M.
Visualization
| Package | Downloads | GitHub Stars | Publication |
|---|---|---|---|
| spiralize: Visualize data on spirals. |  |
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| circlize: circular visualization in R. [#circlize on stackoverflow] |  |
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| ComplexHeatmap: Flexibly arranging multiple heatmaps and self define annotation graphics. |
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| InteractiveComplexHeatmap: Makes interactive ComplexHeatmap. |  |
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| EnrichedHeatmap: Visualizes the enrichment of genomic signals on specific target region. |
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| HilbertCurve: Making 2D Hilbert Curve. |  |
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| gtrellis: genome-level trellis layout. |  |
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| BioCartaImage: BioCarta pathway images. |  |
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Data analysis
| Package | Downloads | GitHub Stars | Publication |
|---|---|---|---|
| sfcurve: 2x2, 3x3 and nxn Space-Filling Curves. |  |
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| simona: Semantic Similarity in Bio-Ontologies. |  |
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| simplifyEnrichment: Simplify functional enrichment results. |  |
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| cola: A Framework for Consensus Partitioning. |  |
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| rGREAT: Client of GREAT analysis. |  |
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| CePa: centrality-based pathway enrichment. |  |
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| YAPSA: Yet Another Package for Signature Analysis. (current maintainer) |  |
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Data packages
| Package | Downloads | GitHub Stars | Publication |
|---|---|---|---|
| GeneSummary: RefSeq Gene Summaries. |  |
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| UniProtKeywords: Keywords from the UniProt database. |  |
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| BioMartGOGeneSets: Gene Ontology Gene Sets from BioMart. |  |
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Teaching
| Package | Downloads | GitHub Stars | Publication |
|---|---|---|---|
| GSEAtraining: Learning gene set enrichment analysis. |  |
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Other tools
| Package | Downloads | GitHub Stars | Publication |
|---|---|---|---|
| pkgndep: Check the Heaviness of Package Dependencies. |  |
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| bsub: Submitter and monitor of LSF cluster. |  |
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| GetoptLong: wrapper of the Perl module Getopt::Long, also provides a simple variable interpolation in R. |
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| GlobalOptions: setting global options in R. |  |
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Perl
| Package | Downloads | GitHub Stars | Publication |
|---|---|---|---|
| rhydrogen: translate comments to documentations in R. | - |  |
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| Microarray::GEO::SOFT: Reading microarray data in SOFT format from GEO database. | - |  |
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| Statistics::Multtest: Control false discovery rate in multiple test problem. | - |  |
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| List::Vectorize: functions to make vectorized calculation easy. | - |  |
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| ngspipeline: NGS pipeline maker. | - |  |
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Books
Package status
| Package | GitHub Actions | CRAN check | bioc-devel | bioc-release | GitHub issues (opened) | GitHub issues (closed) |
|---|---|---|---|---|---|---|
| circlize |  |
- | - |  |
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| spiralize |  |
- | - |  |
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| GetoptLong |  |
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| GlobalOptions |  |
- | - |  |
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| bsub |  |
- | - |  |
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| pkgndep |  |
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| YAPSA | - | - |  |
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| simona |  |
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| simplifyEnrichment |  |
- |  |
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| ComplexHeatmap |  |
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| InteractiveComplexHeatmap |  |
- |  |
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| EnrichedHeatmap |  |
- |  |
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| HilbertCurve |  |
- |  |
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| gtrellis |  |
- |  |
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| rGREAT |  |
- |  |
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| cola |  |
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| GeneSummary |  |
- | - | - |  |
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| UniProtKeywords |  |
- | - | - |  |
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| BioMartGOGeneSets |  |
- | - | - |  |
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| BioCartaImage |  |
- | - | - |  |
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