PoisonAlien/TCGAmutations PoisonAlien/TCGAmutations

  • Stars
    star
    82
  • Rank 396,546 (Top 8 %)
  • Language
    R
  • License
    MIT License
  • Created about 7 years ago
  • Updated 9 months ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
PoisonAlien/TCGAmutations
github

PoisonAlien

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

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

More Repositories

1

maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
R
437
star
2

trackplot

Generate IGV style locus tracks from bigWig files in R
R
129
star
3

basegraphics

Pretty plots using pure base graphics in R
R
78
star
4

somaticfreq

knowledge-based genotyping of cancer hotspots from the tumor BAM files
C
19
star
5

beadAnalyze

Automated differential expression analysis for Illumina beadarrays (HT12 V4 arrays).
R
8
star
6

varscan_accessories

accessory scripts for processing varscan somatic/copynumber outputs.
Python
8
star
7

gtf2fasta

Tookit for gtf format conversion and sequence extraction
Julia
5
star
8

basecounts

A tool to extract ATGC/Indel read counts at user specific loci from BAM files
C
5
star
9

chiptk

optimized protocol for processing 50-bp SE ChIP-seq
Shell
4
star
10

annovar2maf

Tiny python script to generate MAF files from output generated by standard annotation programs
Python
4
star
11

COVID_rXiv

code for Visualizing COVID19 metadata from public sources
R
3
star
12

callpeaks

Bash script to call peaks from MACS2 peak caller
Shell
2
star
13

somatic_pipeline

Python
2
star
14

flatuicoloRs

Color palettes from https://flatuicolors.com/ in R
R
1
star
15

PoisonAlien.github.io

https://poisonalien.github.io/
Ruby
1
star
16

supplementary_code

HTML
1
star
17

squaRify

Minimal, zero dependancy package for drawing treemaps in R
R
1
star