Stephens lab
Research in statistical and computational methods for genetics at the University of Chicago.
Pinned Repositories
dsc
Repo for Dynamic Statistical Comparisons project
ebnm
R package to fit Empirical Bayes Normal Means model.
effective-computing
Effective Computing—Resources for Computational Biologists
fastTopics
Fast algorithms for fitting topic models and non-negative matrix factorizations to count data.
flashr
R package for Empirical Bayes Factor Analysis.
gtexresults
Code and data resources accompanying Urbut et al (2017), "Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions."
ipynb-website
Simple data science website using Jupyter notebooks.
mashr
An R package for multivariate adaptive shrinkage.
rss
Regression with Summary Statistics.
susieR
R package for "sum of single effects" regression.
Stephens lab's Repositories
stephenslab/susieR
R package for "sum of single effects" regression.
stephenslab/mashr
An R package for multivariate adaptive shrinkage.
stephenslab/fastTopics
Fast algorithms for fitting topic models and non-negative matrix factorizations to count data.
stephenslab/flashr
R package for Empirical Bayes Factor Analysis.
stephenslab/rss
Regression with Summary Statistics.
stephenslab/gtexresults
Code and data resources accompanying Urbut et al (2017), "Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions."
stephenslab/mvsusieR
A new model and algorithm for multivariate Bayesian variable selection regression.
stephenslab/dsc
Repo for Dynamic Statistical Comparisons project
stephenslab/ebnm
R package to fit Empirical Bayes Normal Means model.
stephenslab/mixsqp
R package for fast maximum-likelihood estimation of mixture proportions using SQP.
stephenslab/poisson.mash.alpha
An R package for Poisson multivariate adaptive shrinkage.
stephenslab/mr.ash.alpha
An R package implementing Mr.ASH method
stephenslab/udr
R package implementing empirical Bayes methods for multivariate normal means.
stephenslab/finemap-uk-biobank
Code & scripts implementing genetic association and fine-mapping analyses of UK Biobank data.
stephenslab/gradvi
Gradient descent methods for Bayesian variational inference with mean field approximation.
stephenslab/fastglmpca
Fast algorithms for GLM-PCA.
stephenslab/mr.ash
R package implementing methods for multiple regression with adaptive shrinkage priors ("mr.ash").
stephenslab/mr.mash.alpha
R package implementing methods for multivariate multiple regression with adaptive shrinkage priors.
stephenslab/single-cell-topics
Analysis of single-cell RNA-seq data using topic models.
stephenslab/causal-TWAS
website for causal TWAS project
stephenslab/scATACseq-topics
Analysis of single-cell ATAC-seq data using topic models.
stephenslab/fsusieR
Draft package for "Sum of Single Functions" method.
stephenslab/gbcd-workflow
GBCD analyses of scRNA-seq data from malignant cells.
stephenslab/mr-ash-workflow
MR.ASH (Multiple Regression with Adaptive Shrinkage) method and other linear regression methods.
stephenslab/fastTopics-experiments
Numerical experiments on fitting non-negative matrix factorizations and topic models.
stephenslab/gbcd
R package for generalized binary covariance decomposition.
stephenslab/VEB.Boost
R package implementing variational Empirical Bayes boosting methods.
stephenslab/eb-linreg-dsc
stephenslab/ebpm
R package to fit the "Empirical Bayes Poisson Means" model.
stephenslab/mmbr-rss-dsc
mvSuSiE simulation code and results.