https://github.com/poisonalien/maftools

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

bioinformatics cancer-genome-atlas cancer-genomics genomics maf-files r tcga

Last synced: 14 May 2025

https://github.com/poisonalien/trackplot

Generate IGV style locus tracks from bigWig files in R

bigwigs igv-like locus ucsc-browser

Last synced: 05 Apr 2025

https://github.com/poisonalien/tcgamutations

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

ccle maf maftools mutations somatic-variants tcga-data

Last synced: 06 Apr 2025

https://github.com/poisonalien/basegraphics

Pretty plots using pure base graphics in R

Last synced: 08 Apr 2025

https://github.com/poisonalien/somaticfreq

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

bam-files cancer-genomics html-report somatic-mutations

Last synced: 12 May 2025

https://github.com/poisonalien/varscan_accessories

accessory scripts for processing varscan somatic/copynumber outputs.

converts-varscan-somatic copynumber segmentation somatic-variants varscan vcf

Last synced: 12 May 2025

https://github.com/poisonalien/beadanalyze

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

differential-expression idat illumina-beadarrays microarry

Last synced: 12 May 2025

https://github.com/poisonalien/gtf2fasta

Tookit for gtf format conversion and sequence extraction

gtf rna-seq

Last synced: 30 Apr 2025

https://github.com/poisonalien/basecounts

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

bam basecounts bioinformatics nucleotide-frequency readcounts sequencing wgs-data

Last synced: 12 May 2025

https://github.com/poisonalien/chiptk

optimized protocol for processing 50-bp SE ChIP-seq

chip-seq pipeline-runner super-enhancers

Last synced: 12 May 2025

https://github.com/poisonalien/annovar2maf

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

Last synced: 12 May 2025

https://github.com/poisonalien/covid_rxiv

code for Visualizing COVID19 metadata from public sources

Last synced: 30 Mar 2025

https://github.com/poisonalien/somatic_pipeline

Last synced: 15 Apr 2025

https://github.com/poisonalien/callpeaks

Bash script to call peaks from MACS2 peak caller

Last synced: 30 Mar 2025

https://github.com/poisonalien/poisonalien.github.io

https://poisonalien.github.io/

Last synced: 30 Mar 2025

https://github.com/poisonalien/supplementary_code

Last synced: 30 Mar 2025

https://github.com/poisonalien/squarify

Minimal, zero dependancy package for drawing treemaps in R

rstats treemap treemap-diagram visulization

Last synced: 30 Mar 2025

https://github.com/poisonalien/flatuicolors

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

flatui flatuicolors r

Last synced: 30 Mar 2025

https://github.com/poisonalien/star_wrapper_script

Last synced: 30 Mar 2025