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maftools
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.trackplot
Generate IGV style locus tracks from bigWig files in RTCGAmutations
R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)basegraphics
Pretty plots using pure base graphics in Rsomaticfreq
knowledge-based genotyping of cancer hotspots from the tumor BAM filesbeadAnalyze
Automated differential expression analysis for Illumina beadarrays (HT12 V4 arrays).varscan_accessories
accessory scripts for processing varscan somatic/copynumber outputs.gtf2fasta
Tookit for gtf format conversion and sequence extractionbasecounts
A tool to extract ATGC/Indel read counts at user specific loci from BAM fileschiptk
optimized protocol for processing 50-bp SE ChIP-seqannovar2maf
Tiny python script to generate MAF files from output generated by standard annotation programsCOVID_rXiv
code for Visualizing COVID19 metadata from public sourcescallpeaks
Bash script to call peaks from MACS2 peak callerflatuicoloRs
Color palettes from https://flatuicolors.com/ in RPoisonAlien.github.io
https://poisonalien.github.io/supplementary_code
squaRify
Minimal, zero dependancy package for drawing treemaps in RLove Open Source and this site? Check out how you can help us