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    107 repositories

    • fsusieR

      Public
      R package for "Sum of Single Functions" (fSuSiE) with applications to fine-mapping of molecular profiles.
      R
      •
      Other
      •1•7•4•0•Updated Oct 16, 2026Oct 16, 2026

    • mvsusieR

      Public
      A new model and algorithm for multivariate Bayesian variable selection regression.
      Jupyter Notebook
      •
      Other
      •10•34•1•0•Updated Oct 13, 2026Oct 13, 2026

    • susieR

      Public
      R package for "sum of single effects" regression.
      R
      •
      Other
      •62•271•49•6•Updated Oct 11, 2026Oct 11, 2026

    • fashr

      Public
      R package for functional adaptive shrinkage (FASH).
      R
      •0•3•1•0•Updated Oct 4, 2026Oct 4, 2026

    • single-cell-jamboree

      Public
      Exploratory analyses of single-cell data sets using different matrix factorization approaches.
      R
      •0•2•0•0•Updated Sep 16, 2026Sep 16, 2026

    • finemap

      Public
      Demos of SuSiE and FINEMAP.
      R
      •0•2•0•0•Updated Aug 31, 2026Aug 31, 2026

    • fsusie-experiments

      Public
      Code and data for fsusie paper.
      R
      •
      MIT License
      •1•1•0•0•Updated Aug 24, 2026Aug 24, 2026

    • fastTopics-experiments

      Public
      Numerical experiments on fitting non-negative matrix factorizations and topic models.
      R
      •
      MIT License
      •1•2•0•0•Updated Jul 24, 2026Jul 24, 2026

    • fastTopics

      Public
      Fast algorithms for fitting topic models and non-negative matrix factorizations to count data.
      R
      •
      Other
      •12•86•16•1•Updated May 22, 2026May 22, 2026

    • flashier

      Public
      A faster and angrier package for EBMF.
      R
      •
      Other
      •13•0•0•0•Updated May 8, 2026May 8, 2026

    • mr.mashr

      Public
      R package implementing methods for multivariate multiple regression with adaptive shrinkage priors.
      R
      •
      Other
      •6•7•0•0•Updated Feb 16, 2026Feb 16, 2026

    • udr

      Public
      R package implementing empirical Bayes methods for multivariate normal means.
      R
      •
      Other
      •1•8•9•0•Updated Jan 28, 2026Jan 28, 2026

    • fashr-paper

      Public
      The online code repository for FASH (fashr).
      R
      •0•1•0•0•Updated Jan 22, 2026Jan 22, 2026

    • mr.ashr

      Public
      R package implementing methods for multiple regression with adaptive shrinkage priors ("mr.ash").
      R
      •
      Other
      •0•4•6•1•Updated Dec 16, 2025Dec 16, 2025

    • smashr

      Public
      An R package for smoothing & signal denoising using adaptive shrinkage.
      R
      •
      GNU General Public License v3.0
      •7•8•5•0•Updated Dec 15, 2025Dec 15, 2025

    • ebnm

      Public
      R package to fit Empirical Bayes Normal Means model.
      R
      •12•14•17•0•Updated Dec 3, 2025Dec 3, 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•16•10•0•Updated Jul 13, 2025Jul 13, 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•3•0•0•Updated Apr 14, 2025Apr 14, 2025

    • fastglmpca

      Public
      Fast algorithms for GLM-PCA.
      HTML
      •
      GNU General Public License v2.0
      •0•19•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•55•25•1•Updated Dec 4, 2024Dec 4, 2024

    • mashr

      Public
      An R package for multivariate adaptive shrinkage.
      R
      •
      Other
      •22•102•60•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
      projects
      MATLAB
      •
      MIT License
      •11•51•0•1•Updated Sep 16, 2024Sep 16, 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
      •12•14•36•1•Updated Feb 5, 2024Feb 5, 2024
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