Pinned

1. maftools maftools Public

   Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

   R 421 215

2. trackplot trackplot Public

   Generate IGV style locus tracks from bigWig files in R

   R 123 15

3. TCGAmutations TCGAmutations Public

   R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)

   R 76 23

4. basegraphics basegraphics Public

   Pretty plots using pure base graphics in R

   R 72 9

5. somaticfreq somaticfreq Public

   knowledge-based genotyping of cancer hotspots from the tumor BAM files

   C 19 3

6. basecounts basecounts Public

   A tool to extract ATGC/Indel read counts at user specific loci from BAM files

   C 5 1