Stephens lab's repositories
mashr-paper
Multivariate adaptive shrinkage methods used for analysis GTEx data in Urbut et al (2017).
count-clustering
Code and data reproducing results from our PLOS Genetics paper "Visualizing the structure of RNA-seq expression data using grade of membership models"
EbayesThresh
R package for Empirical Bayes thresholding and related methods.
dscr-smash
Source code implementing Gaussian denoising simulations for Xing & Stephens (2016).
EbayesThresh_from_kan
R package for Empirical Bayes thresholding and related methods
EBNM-moderated-t
Code and analyses for the "EBNM" project (Empirical Bayes estimation of normal means, accounting for uncertainty in estimated standard errors).
gtex-zcorr
investigate correlations in gtex z scores
mash-application-immune
Applying mash methods to data from Kim-Hellmuth et al (2017).
pps-cluster
Documentation for the PPS cluster (pps-gateway.uchicago.edu), including the upgrade to Red Hat 7.3 (the "Simple Revitalization Plan")
stephenslab.github.io
Github Pages for the Stephens lab.
ashlar
Workflow template
confounding-polygenic
For discussing work related to confounding vs polygenicity
dashr
R package for Dirichlet adaptive shrinkage and smoothing
DDD
slides for DDD site visit
dsc-blm
DSC benchmark for Bayesian linear models.
dsc-normalmeans
repo for dynamic statistical comparison of normal means methods
dsc-regression
Application of DSC2 framework to a range of regression models.
ebayesthresh2
Work on possible extensions to ebayesthresh—see stephenslab/ebayesthresh.
fast-ash.orig
repo set up to investigate ideas to make ash faster
miximash
MIXtures of Independent components in Multivariate Adaptive SHrinkage ("miximash").
shinydsc
R package and shiny application for exploring and visualizing dsc2 results
simple_site
Minimal tutorial on making a simple website with GitHub Pages
Trans-eQTL
Trans-eQTL joint with Barbara Engelhardt