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1. maftoolsmaftoolsPublic

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

   R 481 224

2. trackplottrackplotPublic

   Generate IGV style locus tracks from bigWig files in R

   R 175 18

3. TCGAmutationsTCGAmutationsPublic

   R data package for pre-compiled somatic mutations from TCGA cohorts and CCLE

   R 98 25

4. basegraphicsbasegraphicsPublic

   Pretty plots using pure base graphics in R

   R 92 10

5. somaticfreqsomaticfreqPublic

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

   C 21 4

6. basecountsbasecountsPublic

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

   C 5 1