jstjohn

John St. John (jstjohn)

2016-09-19 21:45:38 +0800 CST

About jstjohn

Summing up all of jstjohn's repositories they have own repositories and 17 contribute repositories .

jstjohn follows other users and is followed by users.

Data for jstjohn was last updated 2016-09-19 21:45:38 +0800 CST.

jstjohn use C, Perl, Java, C++, Python, R, TeX, D, Shell, Scala, Objective-C, Processing, Makefile, ...

Repository

IntroToStatisticalLearningR-

77 0

Work on Introduction to Statistical Learning

SeqPrep

69

Tool for stripping adaptors and/or merging paired reads with overlap into single reads.

SimSeq

28 0,0

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

KentLib

11

Subset of the kent source libraries (perhaps out of date) that are easily built and installed on OSX and Linux.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 uti

re-pair

5

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

Jellyfish

4

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 cent

mia

2

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.

cscripts

1

Miscalanious C and C++ scripts.

gatk

1

GATK Official Release Repository

GrNMF

1

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

homebrew

1

The missing package manager for OS X.

KinectOrbit

1

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

Contribute

rmate

rmate

251

Edit files from an ssh session in TextMate

pybedtools

pybedtools

101 0,1

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

IntroToStatisticalLearningR-

IntroToStatisticalLearningR-

77 0

Work on Introduction to Statistical Learning

SeqPrep

SeqPrep

69

Tool for stripping adaptors and/or merging paired reads with overlap into single reads.

bamsurgeon

bamsurgeon

62 0,0

tools for adding mutations to existing .bam files, used for testing mutation callers

docker-formula

docker-formula

56 0,0,0,0,0,0,0

Install and set up Docker

avocado

avocado

54 0

A Variant Caller, Distributed. Apache 2 licensed.

SimSeq

SimSeq

28 0,0

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

KentLib

KentLib

11

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 uti

re-pair

re-pair

5

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

Jellyfish

Jellyfish

4

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 cent

mia

mia

2

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.

cscripts

cscripts

1

Miscalanious C and C++ scripts.

gatk

gatk

1

GATK Official Release Repository

GrNMF

GrNMF

1

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

KinectOrbit

KinectOrbit

1

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

CS242

CS242

1

Group materials for CMPS 242