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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

basegraphics

Pretty plots using pure base graphics in R

beadanalyze

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

bwtool

A tool for bigWig files.

callpeaks

Bash script to call peaks from MACS2 peak caller

chipanalyser

chiptk

optimized protocol for processing 50-bp SE ChIP-seq

covid_rxiv

code for Visualizing COVID19 metadata from public sources

echtvar

using all the bits for echt rapid variant annotation and filtering

flatuicolors

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

gtf2fasta

Tookit for gtf format conversion and sequence extraction

maftools

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

noodles

Bioinformatics I/O libraries in Rust

poisonalien.github.io

https://poisonalien.github.io/

projecttemplate

A template utility for R projects that provides a skeletal project.

resprog

Program directory RESPONSIFY

somatic_pipeline

somaticfreq

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

squarify

Minimal, zero dependancy package for drawing treemaps in R

star_wrapper_script

supplementary_code

tcgamutations

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

trackplot

Generate IGV style locus tracks from bigWig files in R

variant_catalogue_pipeline

CAFE pipeline

varscan_accessories

accessory scripts for processing varscan somatic/copynumber outputs.

wgbs_best_practice