vd4mmind

ENCODE_chipseq_pipeline

ENCODE ChIP-seq pipeline

biostar-tutorials

Code for biostar tutorials - mostly R and Perl

idr

IDR

kg

Query KEGG from the command line

MACS

MACS -- Model-based Analysis of ChIP-Seq

ASE_bamreadcount

Allele Specific Expression using bam-readcount

bioawk

BWK awk modified for biological data

ChIP-seq-analysis

chromhmm-tools

Helpers for working with ChromHMM (http://compbio.mit.edu/ChromHMM/)

epiPredictor

filetools

Generic tools for handling plain text and tab-delimited files.

jvarkit

Java utilities for Bioinformatics

Markdown-for-bio-scientists

Draft: presentation about Markdown basics and applications

matplotlib_for_papers

Handout for the tutorial "Creating publication-quality figures with matplotlib"

Microarray_Analysis

Analysis of Microarray data

muts-needle-plot

A needle plot for mutation data

ngCGH

Tools for producing pseudo-cgh of next-generation sequencing data

NGScripts

A variety of scripts useful when working with NGS data and genome assemblies created with NGS data.

phantompeakqualtools

Automatically exported from code.google.com/p/phantompeakqualtools

poverlap

significance testing over interval overlaps

reference-code

Code used in published material like articles or theses.

RNA-Seq

Automated TopHat-cuffdiff pipeline for illumina paired-end data for ran-seq data analysis

RNAvc

Variant calling using RNA-seq data

rpkm_rnaseq_count

RPKM for RNASeq counts

sciclone

An R package for inferring the subclonal architecture of tumors

TCGA

TCGA_work

timeplot

Using R to plot gene expression time course

vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

web-TCGA

A light weight shiny based web app to access TCGA data