Software
R
- pkgndep: Check the Heaviness of Package Dependencies.
- simplifyEnrichment: Simplify functional enrichment results.
- bsub: Submitter and monitor of LSF cluster.
- cola: A Framework for Consensus Partitioning.
- 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.
- rGREAT: Client of GREAT analysis.
- GetoptLong: wrapper of the Perl module Getopt::Long, also provides a simple variable interpolation in R.
- GlobalOptions: setting global options in R.
- CePa: centrality-based pathway enrichment.
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 | travis-ci | bioc-devel | bioc-release |
|---|---|---|---|
| circlize |  |
- | - |
| GetoptLong | |
- | - |
| GlobalOptions | |
- | - |
| bsub | |
- | - |
| pkgndep | |
- | - |
| simplifyEnrichment | |
 |
 |
| ComplexHeatmap | |
 |
|
| InteractiveComplexHeatmap | |
- | - |
| EnrichedHeatmap |  |
|
|
| HilbertCurve | |
|
|
| gtrellis | |
|
|
| rGREAT | |
|
|
| cola | |
|
|