jstjohn

SimSeq

An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . Additionally the program provides the ability to model both site and base specific error, and scripts are provided to train this error model on real datasets. My hope in creating this program is to generate as realistic data as possible to assist in assessing the accuracy of genome assembly tools.

KentLib

Subset of the kent source libraries (perhaps out of date) that are easily built and installed on OSX and Linux. These libraries provide usefull utilities for bioinformatics programming in C. This may contain some of my own libraries for bioinformatics utilities as well as long as they install easily on both my mac and linux box.

GrNMF

An R/Rcpp/RcppArmadillo implementation of Deng Cai's Non-negative Matrix Factorization on Manifold, sometimes called GNMF or GrNMF.

Jellyfish

Fork of the jellyfish kmer counter. Here is the description copied from their site: JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish stats" command. See the documentation below for more details.

re-pair

Program to re-do the pairing of fastq reads. This program is modified from http://code.google.com/p/ngopt/source/browse/trunk/tools/pair_reads/repair.cpp?r=85

cscripts

Miscalanious C and C++ scripts.

mia

MIA is an reference guided assembler for DNA reads as generated by recent sequencing technologies. It is designed to support unusual short reads like they come from ancient, fragmented DNA.

gatk

GATK Official Release Repository

homebrew

The missing package manager for OS X.

KinectOrbit

A fork of http://www.arduinoandkinectprojects.com/kinectorbit with an attempt at upgrading to Processing v2.

adam

A genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.

amazonaccess

Amazon Employee Access Challenge

cloneHD

High-definition reconstruction of clonal composition from next-generation sequencing data

flickribbon

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

fonolo4android

Automatically exported from code.google.com/p/fonolo4android

genefamilyfinder

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

ggplot

ggplot for python

puppet-playground

A Vagrant MultiOS environment to test Puppet code and modules

rmate

seizure-detection

Kaggle competition winning submission for the UPenn and Mayo Clinic's Seizure Detection Challenge

StarCluster

StarCluster is a utility for creating and managing computing clusters hosted on Amazon's Elastic Compute Cloud (EC2).

textmate

TextMate is a graphical text editor for OS X 10.7+