Stephens lab

susieR

R package for "sum of single effects" regression.

mashr

An R package for multivariate adaptive shrinkage.

fastTopics

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

flashr

R package for Empirical Bayes Factor Analysis.

rss

Regression with Summary Statistics.

gtexresults

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

mvsusieR

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

dsc

Repo for Dynamic Statistical Comparisons project

ebnm

R package to fit Empirical Bayes Normal Means model.

mixsqp

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

poisson.mash.alpha

An R package for Poisson multivariate adaptive shrinkage.

mr.ash.alpha

An R package implementing Mr.ASH method

udr

R package implementing empirical Bayes methods for multivariate normal means.

finemap-uk-biobank

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

gradvi

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

mr.ash

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

mr.mash.alpha

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

single-cell-topics

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

causal-TWAS

website for causal TWAS project

scATACseq-topics

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

fastglmpca

Fast algorithms for GLM-PCA.

fsusieR

Draft package for "Sum of Single Functions" method.

gbcd-workflow

GBCD analyses of scRNA-seq data from malignant cells.

mr-ash-workflow

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

fastTopics-experiments

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

gbcd

R package for generalized binary covariance decomposition.

VEB.Boost

R package implementing variational Empirical Bayes boosting methods.

eb-linreg-dsc

ebpm

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

mmbr-rss-dsc

mvSuSiE simulation code and results.