R
Downloads are from CRAN/Bioconductor/anaconda, updated on 2023-03-26.
Total downloads: 4.6M.
Visualization
- spiralize: Visualize data on spirals.
- circlize: circular visualization in R. [#circlize on stackoverflow]
- ComplexHeatmap: Flexibly arranging multiple heatmaps and self define annotation graphics.
- InteractiveComplexHeatmap: Makes interactive ComplexHeatmap.
- EnrichedHeatmap: Visualizes the enrichment of genomic signals on specific target region.
- HilbertCurve: Making 2D Hilbert Curve.
- gtrellis: genome-level trellis layout.
Data analysis
- simplifyEnrichment: Simplify functional enrichment results.
- cola: A Framework for Consensus Partitioning.
- rGREAT: Client of GREAT analysis.
- CePa: centrality-based pathway enrichment.
- GeneSummary: RefSeq Gene Summaries.
- UniProtKeywords: Keywords from the UniProt database.
- BioMartGOGeneSets: Gene Ontology Gene Sets from BioMart.
Other tools
- pkgndep: Check the Heaviness of Package Dependencies.
- bsub: Submitter and monitor of LSF cluster.
- GetoptLong: wrapper of the Perl module Getopt::Long, also provides a simple variable interpolation in R.
- GlobalOptions: setting global options in R.
Perl
- rhydrogen: translate comments to documentations in R.
- Microarray::GEO::SOFT: Reading microarray data in SOFT format from GEO database.
- Statistics::Multtest: Control false discovery rate in multiple test problem.
- List::Vectorize: functions to make vectorized calculation easy.
- ngspipeline: NGS pipeline maker.
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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| 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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