vd4mmind

RNA-seq-analysis

AfterQC

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

bioinformatics-cafe

Unsorted scripts for bioinformatics. Former google.code bioinformatics-misc

bioinformatics-hacks

A collection of Python scripts I use for random bioinformatics-related tasks.

bpipe

Bpipe - a tool for running and managing bioinformatics pipelines

DansProcessingPipeline

DEGandMore

Analyses related to differential gene expression and functional annotation

epic

diffuse domain ChIP-Seq caller based on SICER

fishplot

Create timecourse "fish plots" that show changes in the clonal architecture of tumors

GenVisR

Genome data visualizations

HaveYouSwappedYourSamples

This project contains simple methods to measure sample relatedness and identify potential swaps and contamination

methylkit

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

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

oneliners

Useful bash one-liners for bioinformatics.

PARE

PARE: a computational method to Predict Active Regulatory Elements

Perl-for-Bioinformatics

An attempt to help anyone interested in using Perl for Bioinformatics

picardmetrics

:vertical_traffic_light: Run Picard and collate multiple metrics.

pysam

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

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

RSkittleBrewer

for those times you want to make plots with candy-themed color schemes

SciRNotebook

Template for building a lab notebook using RMarkdown

SICERpy

Python wrapper around the popular ChIP-Seq peak caller SICER

STAR

RNA-seq aligner

systemPipeR

NGS workflow environment

trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly

TS

Torrent Suite

tximport

Import and summarize transcript-level estimates for gene-level analysis

ubu

UNC-Chapel Hill Bioinformatics Utilities

UpSetR

An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..

work_setup

Different workstation related setups