admixture

Simple accelerated EM implementation of the ADMIXTURE model in R, plus extensions.

archaic

Exploration, clustering, visualization and classification of DNA damage patterns

b6d2muscle

R code implementing QTL mapping of hindlimb muscle weights in C57BL/6J ("B6") x DBA/2J ("D2") mouse advanced intercross line.

binder_test

Specifying a conda environment with `environment.yml`

bmapathway

MATLAB source code to accompany the PLoS Genetics paper, "Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn's disease".

breedail

R code to select breeders from an advanced intercross line so that they minimize inbreeding in the offspring

cars

cehg16-workshop

Demos for AncestryDNA workshop at 2016 CEHG Symposium, Stanford University.

cfw

R code implementing QTL mapping of physiological, behavioral and gene expression phenotypes in Carworth Farms White (CFW) outbred mice.

cfwlab

R package containing data from CFW genome-wide association study for use in courses.

cnmf

Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data

colab

Explorations of the Google Colaboratory.

corshrink

R package for adaptive correlation and covariance matrix shrinkage: Go to the Workflow page here

ctwas

package for the causal TWAS project

dap

software package for integrative genetic association analysis

dataviz

A book covering the fundamentals of data visualization.

dlbayes

Scalable Bayesian variable selection

dogs

Minimal illustration of Binder for sharing a data analysis in R.

dotfiles

Files for setting up shell environment on my MacBook and the compute clusters I regularly use.

dscr

Dynamic statistical comparisons in R.

extreme-deconvolution

Density estimation using Gaussian mixtures in the presence of noisy, heterogeneous and incomplete data

flash_workflow

work flow framework of flash project

flashier

A faster and angrier package for EBMF. In progress.

genetic-data-analysis-rcc-1

Research Computing Center introduction to analysis and visualization of genetic data, Part 1

genetic-data-analysis-rcc-2

Research Computing Center introduction to analysis and visualization of genetic data, Part 2

genotype

Various scripts and functions for manipulating genetic data.

git-intro

My notes from the Intro to Git tutorial in Sep 2019.

git2r

R bindings to the libgit2 library

gtex

Exploratory analyses of GTEx data.

gtexresults_matrixash

Repo for reproducing GTEx results in Urbut et al, 2017 "Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions"