Pinned Repositories
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).
maftools
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
somaticfreq
knowledge-based genotyping of cancer hotspots from the tumor BAM files
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
varscan_accessories
accessory scripts for processing varscan somatic/copynumber outputs.
PoisonAlien's Repositories
PoisonAlien/maftools
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
PoisonAlien/trackplot
Generate IGV style locus tracks from bigWig files in R
PoisonAlien/TCGAmutations
R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)
PoisonAlien/basegraphics
Pretty plots using pure base graphics in R
PoisonAlien/somaticfreq
knowledge-based genotyping of cancer hotspots from the tumor BAM files
PoisonAlien/beadAnalyze
Automated differential expression analysis for Illumina beadarrays (HT12 V4 arrays).
PoisonAlien/varscan_accessories
accessory scripts for processing varscan somatic/copynumber outputs.
PoisonAlien/basecounts
A tool to extract ATGC/Indel read counts at user specific loci from BAM files
PoisonAlien/chiptk
optimized protocol for processing 50-bp SE ChIP-seq
PoisonAlien/gtf2fasta
Tookit for gtf format conversion and sequence extraction
PoisonAlien/annovar2maf
Tiny python script to generate MAF files from output generated by standard annotation programs
PoisonAlien/COVID_rXiv
code for Visualizing COVID19 metadata from public sources
PoisonAlien/callpeaks
Bash script to call peaks from MACS2 peak caller
PoisonAlien/ProjectTemplate
A template utility for R projects that provides a skeletal project.
PoisonAlien/somatic_pipeline
PoisonAlien/chipAnalyser
PoisonAlien/flatuicoloRs
Color palettes from https://flatuicolors.com/ in R
PoisonAlien/PoisonAlien.github.io
https://poisonalien.github.io/
PoisonAlien/squaRify
Minimal, zero dependancy package for drawing treemaps in R
PoisonAlien/supplementary_code
PoisonAlien/WGBS_best_practice
PoisonAlien/bwtool
A tool for bigWig files.
PoisonAlien/echtvar
using all the bits for echt rapid variant annotation and filtering
PoisonAlien/noodles
Bioinformatics I/O libraries in Rust
PoisonAlien/RESprog
Program directory RESPONSIFY
PoisonAlien/STAR_wrapper_script
PoisonAlien/Variant_catalogue_pipeline
CAFE pipeline