Mainly using R as the programming language. Total downloads ~ 9.7M. Data is from CRAN / Bioconductor / Anaconda. Updated on 2025-12-03.
Visualization
| Package | downloads | github | publication |
|---|---|---|---|
| circlize: Circular Visualization. |  |
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| ComplexHeatmap: Complex Heatmap Visualization. |  |
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| InteractiveComplexHeatmap: Make Interactive Complex Heatmap. |  |
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| EnrichedHeatmap: Enrichment of Genomic Signals on Target Region. |  |
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| HilbertCurve: Make 2D Hilbert Curve. |  |
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| spiralize: Visualize Data on Spirals. |  |
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| gtrellis:Genome-level Trellis Layout. |  |
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| BioCartaImage: BioCarta Pathway Images. |  |
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Modeling and Analysis
| Package | downloads | github | 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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Annotation and Data Packages
| Package | downloads | github |
|---|---|---|
| GeneSummary: RefSeq Gene Summaries. |  |
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| UniProtKeywords: Keywords from UniProt. |  |
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| BioMartGOGeneSets: Gene Ontology Gene Sets from BioMart. |  |
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| IlluminaHumanMethylationEPICv2anno.20a1.hg38: Epic Array v2 Annotation. |  |
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| IlluminaHumanMethylationEPICv2manifest: Epic Array v2 Manifest. |  |
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Utility Tools
| Package | downloads | github | publication |
|---|---|---|---|
| pkgndep: Heaviness of Package Dependencies. |  |
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| bsub: Submitter and Monitor of LSF Clusters. |  |
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| GetoptLong: Command-line Argument Parser. |  |
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| GlobalOptions: Set Global Options. |  |
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Teaching
| Package | github |
|---|---|
| GSEAtopics: Various Topics in Gene Set Enrichment Analysis. |  |
Online Books
Status of Packages
| Package | 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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| 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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| IlluminaHumanMethylationEPICv2anno.20a1.hg38 | - | - | - |  |
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| IlluminaHumanMethylationEPICv2manifest | - | - | - |  |
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