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addictioncourse2015

Code and data (or links to data) for Elissa Chesler's Addiction Course in August 2015.

alntools

Preprocess bam file into a compressed alignment incidence matrix (equivalence class)

aseqtl

Allele-specific expression QTL (aseQTL) package

attiemetabolomics

Code for the Attie lab metabolite and lipid data

cc_proteins

CC Protein Viewer. THERE IS CURRENTLY NO DOCUMENTATION.

desnp

Tools for the CGD DeSNPing pipeline

do

Xingyao Chen's work with the DO, summer 2016

emase

Expectation-Maximization algorithm for Allele-Specific Expression

emase-zero

C++ Implementation of EMASE

ensimpl

Simple API into Ensembl

ensimpl_snps

ensimplr

ensimplr-old

Simple R API into ensimpl data

factorial-experiment-viewer

fasta_compare

Compare Fasta Files

g2gtools

Personal diploid genome creation and coordinate conversion

gbrs

Genotype-free genome reconstruction and ASE quantification

how-to-guide

A how-to guide to the Churchill Lab, The Jackson Laboratory, and Bar Harbor.

ibangs2016

DOQTL tutorial for IBANGS 2016

imageechelon

Tool to quantify images where meaningful differences are discernible by eye, but difficult to quantify using traditional methods.

intermediate

small R utility for mediation analysis

j-qtl

J/qtl

kallisto

Near-optimal RNA-Seq quantification

kallisto-align

Export kallisto pseudo-alignments in a sparse binary matrix format

mdibl_aging2016

Benzene QTL example for MDIBL Aging Course

mouse-div-geno

mouse_map_converter

mousegen2016

21st Century Mouse Genetics

msbwt

A python toolkit for building and querying multi-string BWTs

msu_ngs2015

DE analysis module for Week3