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    131 repositories

    • gReLU

      Public
      gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
      Python
      •
      MIT License
      •50•313•23•5•Updated Jan 9, 2026Jan 9, 2026

    • phase1b

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

    • nfnull

      Public
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Jan 6, 2026Jan 6, 2026

    • decima-applications

      Public
      Jupyter Notebook
      •
      Other
      •1•10•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 without additional training.
      Python
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      Other
      •20•232•19•0•Updated Jan 2, 2026Jan 2, 2026

    • jmpost

      Public
      R
      •4•17•55•1•Updated Jan 1, 2026Jan 1, 2026

    • decima

      Public
      Decima is a Python library to train sequence models on single-cell RNA-seq data.
      Python
      •
      Other
      •8•59•2•0•Updated Dec 25, 2025Dec 25, 2025

    • 2025_heinlein_etal

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

    • BayesERtools

      Public
      R
      •
      Other
      •2•6•3•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 precomputed gene attribution scores.
      Python
      •
      Other
      •4•22•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

    • covtracer

      Public
      Tools for contextualizing tests, built using covr test traces.
      R
      •
      Other
      •4•23•10•0•Updated Dec 8, 2025Dec 8, 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•6•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

    • checked

      Public
      batch R CMD check management
      rchecksrevdeps
      R
      •
      Other
      •1•8•13•0•Updated Oct 31, 2025Oct 31, 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
      •2•29•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

    • TimeSeriesExplainabilityData

      Public
      0•0•0•0•Updated Sep 29, 2025Sep 29, 2025

    • PerturbQA

      Public
      Python
      •
      Other
      •3•36•0•0•Updated Sep 23, 2025Sep 23, 2025

    • deepevfi

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Sep 17, 2025Sep 17, 2025

    • rnacounts

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Sep 5, 2025Sep 5, 2025

    • spex_frontend

      Public
      JavaScript
      •
      Other
      •0•0•0•0•Updated Sep 4, 2025Sep 4, 2025

    • beignet

      Public
      A standard library for biological research.
      Python
      •
      MIT License
      •8•31•30•0•Updated Sep 2, 2025Sep 2, 2025