Pinned

1. maftools Public

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

   R 349 202

2. TCGAmutations Public

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

   R 60 20

3. trackplot Public

   Generate IGV style locus tracks from bigWig files in R

   R 63 8

4. CompEpigen/methrix Public

   An R 📦 for fast and flexible DNA methylation analysis

   R 21 9

5. somaticfreq Public

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

   C 14 3

6. basecounts Public

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

   C 4 1