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    106 repositories

    • single-cell-jamboree

      Public
      Exploratory analyses of single-cell data sets using different matrix factorization approaches.
      R
      •0•1•0•0•Updated Dec 14, 2025Dec 14, 2025

    • fashr-paper

      Public
      The online code repository for FASH (fashr).
      R
      •0•1•0•0•Updated Dec 12, 2025Dec 12, 2025

    • mr.mashr

      Public
      R package implementing methods for multivariate multiple regression with adaptive shrinkage priors.
      R
      •
      Other
      •3•5•0•0•Updated Dec 12, 2025Dec 12, 2025

    • fsusieR

      Public
      R package for "Sum of Single Functions" (fSuSiE) with applications to fine-mapping of molecular profiles.
      HTML
      •
      Other
      •1•7•4•2•Updated Dec 12, 2025Dec 12, 2025

    • fashr

      Public
      R package for functional adaptive shrinkage (FASH).
      R
      •0•2•1•0•Updated Dec 10, 2025Dec 10, 2025

    • smashr

      Public
      An R package for smoothing & signal denoising using adaptive shrinkage.
      R
      •
      GNU General Public License v3.0
      •5•6•3•0•Updated Dec 9, 2025Dec 9, 2025

    • susieR

      Public
      R package for "sum of single effects" regression.
      R
      •
      Other
      •53•238•94•2•Updated Dec 5, 2025Dec 5, 2025

    • mvsusieR

      Public
      A new model and algorithm for multivariate Bayesian variable selection regression.
      Jupyter Notebook
      •
      Other
      •8•23•25•1•Updated Dec 4, 2025Dec 4, 2025

    • ebnm

      Public
      R package to fit Empirical Bayes Normal Means model.
      R
      •10•13•13•0•Updated Dec 3, 2025Dec 3, 2025

    • fastTopics

      Public
      Fast algorithms for fitting topic models and non-negative matrix factorizations to count data.
      R
      •
      Other
      •10•84•16•1•Updated Oct 21, 2025Oct 21, 2025

    • fsusie-experiments

      Public
      Code and data for fsusie paper.
      R
      •
      MIT License
      •1•0•0•0•Updated Aug 19, 2025Aug 19, 2025

    • singlecelljamboreeR

      Public
      R package supporting the analyses in the "single-cell jamboree".
      R
      •
      Other
      •0•1•0•0•Updated Aug 15, 2025Aug 15, 2025

    • gbcd

      Public
      R package for generalized binary covariance decomposition.
      R
      •
      Other
      •2•13•8•0•Updated Jul 13, 2025Jul 13, 2025

    • fastTopics-experiments

      Public
      Numerical experiments on fitting non-negative matrix factorizations and topic models.
      R
      •
      MIT License
      •1•2•0•0•Updated Jul 1, 2025Jul 1, 2025

    • reading_lists

      Public
      a repo for reading lists related to research in the Stephens lab
      R
      •1•2•0•0•Updated May 23, 2025May 23, 2025

    • flashierX

      Public
      Flashier extensions.
      R
      •0•0•0•0•Updated Apr 17, 2025Apr 17, 2025

    • VEB.Boost

      Public
      R package implementing variational Empirical Bayes boosting methods.
      R
      •
      MIT License
      •0•2•0•0•Updated Apr 14, 2025Apr 14, 2025

    • fastglmpca

      Public
      Fast algorithms for GLM-PCA.
      HTML
      •
      GNU General Public License v2.0
      •0•14•2•0•Updated Mar 12, 2025Mar 12, 2025

    • gradvi

      Public
      Gradient descent methods for Bayesian variational inference with mean field approximation.
      Python
      •
      MIT License
      •0•8•0•0•Updated Dec 4, 2024Dec 4, 2024

    • flashr

      Public
      R package for Empirical Bayes Factor Analysis.
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •11•51•25•1•Updated Dec 4, 2024Dec 4, 2024

    • mashr

      Public
      An R package for multivariate adaptive shrinkage.
      R
      •
      Other
      •22•91•59•0•Updated Nov 7, 2024Nov 7, 2024

    • gbcd-workflow

      Public
      GBCD analyses of scRNA-seq data from malignant cells.
      HTML
      •
      MIT License
      •1•2•2•1•Updated Sep 25, 2024Sep 25, 2024

    • rss

      Public
      RSS: Regression with Summary Statistics
      projects
      MATLAB
      •
      MIT License
      •11•51•0•1•Updated Sep 16, 2024Sep 16, 2024

    • udr

      Public
      R package implementing empirical Bayes methods for multivariate normal means.
      R
      •
      Other
      •1•8•9•0•Updated May 28, 2024May 28, 2024

    • poisson.mash.alpha

      Public
      An R package for Poisson multivariate adaptive shrinkage.
      R
      •
      Other
      •1•11•1•0•Updated Apr 15, 2024Apr 15, 2024

    • mmbr-rss-dsc

      Public
      mvSuSiE simulation code and results.
      R
      •0•0•0•0•Updated Feb 5, 2024Feb 5, 2024

    • dsc

      Public
      Repo for Dynamic Statistical Comparisons project
      HTML
      •
      MIT License
      •11•13•35•0•Updated Feb 5, 2024Feb 5, 2024

    • mixsqp

      Public
      R package for fast maximum-likelihood estimation of mixture proportions using SQP.
      R
      •
      Other
      •6•11•7•0•Updated Dec 21, 2023Dec 21, 2023

    • mr.ash.alpha

      Public
      An R package implementing Mr.ASH method
      R
      •
      Other
      •2•11•4•0•Updated Oct 31, 2023Oct 31, 2023

    • mr.ash

      Public
      R package implementing methods for multiple regression with adaptive shrinkage priors ("mr.ash").
      R
      •
      Other
      •0•4•5•1•Updated Oct 27, 2023Oct 27, 2023