Anand Mayakonda

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

trackplot. Generate IGV style locus tracks from bigWig files in R

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

basegraphics. Pretty plots using pure base graphics in R

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

varscan_accessories. accessory scripts for processing varscan somatic/copynumber outputs.

beadAnalyze. Automated differential expression analysis for Illumina beadarrays (HT12 V4 arrays).

annovar2maf. Tiny python script to generate MAF files from output generated by standard annotation programs

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

chiptk. optimized protocol for processing 50-bp SE ChIP-seq

gtf2fasta. Tookit for gtf format conversion and sequence extraction

genomics-introduction. Slide decks for introduction to genomics

COVID_rXiv. code for Visualizing COVID19 metadata from public sources

somatic_pipeline. Python

callpeaks. Bash script to call peaks from MACS2 peak caller

flatuicoloRs. Color palettes from https://flatuicolors.com/ in R

PoisonAlien.github.io. https://poisonalien.github.io/

supplementary_code. HTML

squaRify. Minimal, zero dependancy package for drawing treemaps in R