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    138 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 Apr 24, 2026Apr 24, 2026

    • BayesERtools

      Public
      R
      •
      Other
      •4•6•4•0•Updated Apr 23, 2026Apr 23, 2026

    • jmpost

      Public
      R
      •4•17•55•2•Updated Apr 22, 2026Apr 22, 2026

    • IHC-reaction-diffusion

      Public
      Code associated with Perng et al., "Practical quantification of immunohistochemistry antigen concentrations and reaction-diffusion parameters"
      antibodyreaction-diffusionimmunohistochemistry
      antibodyreaction-diffusionimmunohistochemistry
      MATLAB
      •
      MIT License
      •0•0•0•0•Updated Apr 21, 2026Apr 21, 2026

    • 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•24•0•0•Updated Apr 16, 2026Apr 16, 2026

    • gReLU

      Public
      gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
      Python
      •
      MIT License
      •53•323•21•4•Updated Apr 14, 2026Apr 14, 2026

    • MoCAVI

      Public
      Python
      •
      Other
      •0•1•0•0•Updated Apr 14, 2026Apr 14, 2026

    • SpatialAgent

      Public
      An AI agent for spatial biology
      Python
      •
      MIT License
      •23•167•1•0•Updated Apr 13, 2026Apr 13, 2026

    • checked

      Public
      batch R CMD check management
      rchecksrevdeps
      rchecksrevdeps
      R
      •
      Other
      •1•8•15•0•Updated Apr 10, 2026Apr 10, 2026

    • 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•45•1•0•Updated Apr 8, 2026Apr 8, 2026

    • compbiobench-runner

      Public
      CompBioBench: A benchmark of 100 diverse, verifiable questions for agents for computational biology (scripts for running agents)
      Python
      •
      MIT License
      •5•25•0•0•Updated Apr 6, 2026Apr 6, 2026

    • SpatialQPFs

      Public
      R
      •0•5•0•0•Updated Apr 1, 2026Apr 1, 2026

    • Move37

      Public
      Move37 is a data-driven scheduling and resource management system for maximising throughput for individuals and teams
      Python
      •5•2•19•4•Updated Mar 24, 2026Mar 24, 2026

    • decima

      Public
      Decima is a Python library to train sequence models on single-cell RNA-seq data.
      Python
      •
      Other
      •8•65•1•0•Updated Mar 20, 2026Mar 20, 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
      •28•245•20•2•Updated Mar 14, 2026Mar 14, 2026

    • nfnull

      Public
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Mar 2, 2026Mar 2, 2026

    • gReLU-applications

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

    • PerturbView

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

    • covtracer

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

    • barcall

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

    • struct2query

      Public
      Struct2Query: Generates composite molecule queries for virtual screening by searching structurally similar protein binding sites and constructing ROCS queries f…
      Python
      •
      MIT License
      •0•1•0•0•Updated Dec 22, 2025Dec 22, 2025

    • 2025_heinlein_etal

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

    • 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
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