Stephens lab

ebnm

R package to fit Empirical Bayes Normal Means model.

fastglmpca

Fast algorithms for GLM-PCA.

mr.mash.alpha

R package implementing methods for multivariate multiple regression with adaptive shrinkage priors.

udr

R package implementing empirical Bayes methods for multivariate normal means.

gbcd-workflow

GBCD analyses of scRNA-seq data from malignant cells.

gbcd

R package for generalized binary covariance decomposition.

mvsusieR

A new model and algorithm for multivariate Bayesian variable selection regression.

poisson.mash.alpha

An R package for Poisson multivariate adaptive shrinkage.

fastTopics

Fast algorithms for fitting topic models and non-negative matrix factorizations to count data.

susieR

R package for "sum of single effects" regression.

fsusieR

Draft package for "Sum of Single Functions" method.

mmbr-rss-dsc

mvSuSiE simulation code and results.

dsc

Repo for Dynamic Statistical Comparisons project

flashr

R package for Empirical Bayes Factor Analysis.

mixsqp

R package for fast maximum-likelihood estimation of mixture proportions using SQP.

mr.ash.alpha

An R package implementing Mr.ASH method

mr.ash

R package implementing methods for multiple regression with adaptive shrinkage priors ("mr.ash").

fastTopics-experiments

Numerical experiments on fitting non-negative matrix factorizations and topic models.

mashr

An R package for multivariate adaptive shrinkage.

ebpm

R package to fit the "Empirical Bayes Poisson Means" model.

finemap-uk-biobank

Code & scripts implementing genetic association and fine-mapping analyses of UK Biobank data.

rss

Regression with Summary Statistics.

mr-ash-workflow

MR.ASH (Multiple Regression with Adaptive Shrinkage) method and other linear regression methods.

causal-TWAS

website for causal TWAS project

VEB.Boost

R package implementing variational Empirical Bayes boosting methods.

scATACseq-topics

Analysis of single-cell ATAC-seq data using topic models.

single-cell-topics

Analysis of single-cell RNA-seq data using topic models.

gradvi

Gradient descent methods for Bayesian variational inference with mean field approximation.

gtexresults

Code and data resources accompanying Urbut et al (2017), "Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions."

eb-linreg-dsc