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admix-simu

Program to simulate admixture between multiple populations

ancestry_pipeline

Provides helper scripts for inferring local ancestry, performing ancestry-specific PCA, etc

awesome-seq

ballgown_code

analysis code used in Ballgown paper

bismarkmultimappinglocations

This is a side-project of Bismark whose aim is to output multiply mapping read positions without any of the methylation specific features.

bspat

bisulfite sequencing pattern analysis tool

chip-seq-analysis

ChIP-seq analysis notes from Tommy Tang

ckeditor-dev

The development repository of CKEditor.

courseradatascience

courses

Course materials for the Data Science Specialization: https://www.coursera.org/specialization/jhudatascience/1

datascience

datasciencecoursera

datasharing

The Leek group guide to data sharing

deeptools

Tools to process and analyze deep sequencing data.

ea-utils

Automatically exported from code.google.com/p/ea-utils

efficientr

Efficient R programming: a book

fastx-mutate-tools

some simple tools to introduce SNPs/indels/bisulfite conversions in fastq/fasta files

fluff

Fluff is a Python package that contains several scripts to produce pretty, publication-quality figures for next-generation sequencing experiments.

ggplot

ggplot implementation in java for easy graphing based on the grammar of graphics and ggplot2

github-for-developers-7

gradschool-bioinformatics

A collection of bioinformatics hacks (Perl/Java) from graduate school.

hihmm

hiHMM: Bayesian non-parametric joint inference of chromatin state maps

htsjdk

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

intermine

A powerful open source data warehouse system

java-genomics-toolkit

Collection of scripts for working with Wiggle files and analyzing sequencing data

jobberbase

Jobberbase is open-source job board software http://www.jobberbase.com

jobskee-open-source-job-board

Jobskee is an open source job board built using PHP and MySQL (http://jobskee.com)

jvarkit

Java utilities for Bioinformatics

knitr-examples

a collection of knitr examples

methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.