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affytemplate

R scripts for processing Affy arrays

agilentonecolortemplate

R script for processing one color agilent arrays

agilenttwocolortemplate

Normalization script for Agilent Two color Arrays

arnold-syntax-highlighter

The Arnold Syntax Highlighter modules makes it easier to compose and edit Solid Angle Arnold scene source (.ASS) files.

bcbb

Incubator for useful bioinformatics code, primarily in Python and R

bcbio-nextgen

Validated, scalable, community developed variant calling and RNA-seq analysis

bioinformatics_liu

biojava

:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java framework for processing biological data.

biopython

Official git repository for Biopython (converted from CVS)

egc.tools

USC Epigenome Center packaging tools for TCGA

fasd

Command-line productivity booster, offers quick access to files and directories, inspired by autojump, z and v.

gatk-protected

GATK Official Release Repository: contains the core MIT-licensed GATK framework, plus "protected" tools restricted to non-commercial use only

glioblastoma-exploration

Scouring the Glioblastoma (GBM) TCGA expression data for molecular signatures indicative of survival benefit

goagent

https://code.google.com/p/goagent/issues/list

htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

metaicb

mirnaannotationtools

Bioconductor annotation packages for microRNAs (mirbase, targetscan)

molokai

Molokai color scheme for Vim

oh-my-emacs

Provide an awesome, out-of-box, literate dotemacs for both newbies and nerds.

pathway

picard

A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.

prelude

Prelude is an enhanced Emacs 24 distribution that should make your experience with Emacs both more pleasant and more powerful.

r-scripts-for-microarray-processing

rcode

for bioinformatics

rnaseq_workflow

TCGA_RNA seq workflow

snip

spf13-vim

The ultimate vim distribution

stock_test

synapsetcgapancan

Scripts for creating figures for TCGA pan cancer datasets

teachingmaterial

Various teaching material