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    134 repositories

    • scallops

      Public
      SCALLOPS (Scalable Library for Optical Pooled Screens) is a comprehensive Python package designed to streamline and scale the analysis of Optical Pooled Screens…
      Python
      •
      Other
      •0•2•0•1•Updated Feb 18, 2026Feb 18, 2026

    • checked

      Public
      batch R CMD check management
      rchecksrevdeps
      R
      •
      Other
      •1•8•12•1•Updated Feb 18, 2026Feb 18, 2026

    • SpatialAgent

      Public
      An AI agent for spatial biology
      Python
      •
      MIT License
      •15•140•0•1•Updated Feb 17, 2026Feb 17, 2026

    • jmpost

      Public
      R
      •4•17•55•2•Updated Feb 15, 2026Feb 15, 2026

    • gReLU-applications

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Feb 7, 2026Feb 7, 2026

    • penrose-lamarck

      Public
      Python
      •0•0•15•0•Updated Feb 6, 2026Feb 6, 2026

    • PerturbView

      Public
      Python
      •
      MIT License
      •1•4•1•0•Updated Feb 6, 2026Feb 6, 2026

    • decima

      Public
      Decima is a Python library to train sequence models on single-cell RNA-seq data.
      Python
      •
      Other
      •8•63•0•0•Updated Feb 5, 2026Feb 5, 2026

    • covtracer

      Public
      Tools for contextualizing tests, built using covr test traces.
      R
      •
      Other
      •4•23•10•0•Updated Jan 30, 2026Jan 30, 2026

    • gReLU

      Public
      gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
      Python
      •
      MIT License
      •50•315•23•3•Updated Jan 29, 2026Jan 29, 2026

    • barcall

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Jan 20, 2026Jan 20, 2026

    • nfnull

      Public
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Jan 14, 2026Jan 14, 2026

    • phase1b

      Public
      R
      •
      Other
      •4•11•17•1•Updated Jan 6, 2026Jan 6, 2026

    • decima-applications

      Public
      Jupyter Notebook
      •
      Other
      •1•11•0•0•Updated Jan 5, 2026Jan 5, 2026

    • LNPseqR

      Public
      Repository with an R package containing an R Markdown script and raw data for the LNP-seq manuscript.
      R
      •
      Other
      •0•0•0•0•Updated Jan 5, 2026Jan 5, 2026

    • equivariance_learning

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jan 5, 2026Jan 5, 2026

    • scimilarity

      Public
      A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies witho…
      Python
      •
      Other
      •22•234•19•0•Updated Jan 2, 2026Jan 2, 2026

    • 2025_heinlein_etal

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Dec 20, 2025Dec 20, 2025

    • BayesERtools

      Public
      R
      •
      Other
      •2•6•4•0•Updated Dec 18, 2025Dec 18, 2025

    • BayesERbook

      Public
      R
      •
      Other
      •1•4•1•1•Updated Dec 16, 2025Dec 16, 2025

    • secretome_dictionary

      Public
      0•0•0•0•Updated Dec 15, 2025Dec 15, 2025

    • SIGnature

      Public
      SIGnature is a Python package that empowers researchers to rapidly query gene sets across diverse single-cell RNA sequencing (scRNA-seq) datasets through precom…
      Python
      •
      Other
      •4•23•0•0•Updated Dec 12, 2025Dec 12, 2025

    • opentreesearch

      Public
      LLM-Guided Code Evolution
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 10, 2025Dec 10, 2025

    • tangram2

      Public
      Jupyter Notebook
      •
      Other
      •0•3•0•1•Updated Dec 8, 2025Dec 8, 2025

    • CLADD

      Public
      The official source code for "RAG-Enhanced Collaborative LLM Agents for Drug Discovery"
      Python
      •
      Other
      •2•10•0•0•Updated Nov 13, 2025Nov 13, 2025

    • modsculpt

      Public
      Direct and Indirect Additive Modeling with Model Sculpting
      R
      •
      Apache License 2.0
      •0•0•1•0•Updated Nov 10, 2025Nov 10, 2025

    • gneprop

      Public
      GNEprop is a graph neural network-based model to predict antibacterial activity from molecular structures in virtual screening settings.
      Jupyter Notebook
      •
      Other
      •5•39•3•0•Updated Oct 30, 2025Oct 30, 2025

    • set-dino

      Public
      Python
      •
      Apache License 2.0
      •2•4•0•0•Updated Oct 23, 2025Oct 23, 2025

    • SpatialQPFs

      Public
      R
      •0•3•0•0•Updated Oct 19, 2025Oct 19, 2025

    • spex-tools

      Public
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Oct 17, 2025Oct 17, 2025