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    122 repositories

    • gneprop

      Public
      GNEprop is a graph neural network-based model to predict antibacterial activity from molecular structures in virtual screening settings.
      Python
      •
      Other
      •0•6•1•0•Updated Aug 8, 2025Aug 8, 2025

    • gReLU

      Public
      gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
      Python
      •
      MIT License
      •42•269•22•7•Updated Aug 7, 2025Aug 7, 2025

    • spex-tools

      Public
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Aug 2, 2025Aug 2, 2025

    • nfnull

      Public
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Aug 1, 2025Aug 1, 2025

    • jmpost

      Public
      R
      •4•17•54•1•Updated Aug 1, 2025Aug 1, 2025

    • phase1b

      Public
      R
      •
      Other
      •4•11•14•1•Updated Jul 31, 2025Jul 31, 2025

    • decima

      Public
      Decima is a Python library to train sequence models on single-cell RNA-seq data.
      Jupyter Notebook
      •
      Other
      •8•42•3•1•Updated Jul 28, 2025Jul 28, 2025

    • checked

      Public
      batch R CMD check management
      rchecksrevdeps
      R
      •
      Other
      •1•8•15•1•Updated Jul 24, 2025Jul 24, 2025

    • beignet

      Public
      A standard library for biological research.
      Jupyter Notebook
      •
      MIT License
      •7•28•29•29•Updated Jul 22, 2025Jul 22, 2025

    • sc_simvar

      Public
      Python
      •
      Other
      •0•1•0•0•Updated Jul 16, 2025Jul 16, 2025

    • BayesERtools

      Public
      R
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      Other
      •1•6•4•1•Updated Jul 7, 2025Jul 7, 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
      •0•4•0•0•Updated Jul 4, 2025Jul 4, 2025

    • BRAID

      Public
      BRAID is a department within Genentech dedicated to advancing biological and clinical sciences through artificial intelligence.
      9•207•0•0•Updated Jun 26, 2025Jun 26, 2025

    • 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
      •13•211•18•0•Updated Jun 26, 2025Jun 26, 2025

    • BayesERbook

      Public
      R
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      Other
      •1•3•1•0•Updated Jun 25, 2025Jun 25, 2025

    • psborrow

      Public
      An R package for Bayesian Dynamic Borrowing. Check out the successor psborrow2: https://github.com/Genentech/psborrow2
      HTML
      •
      Other
      •3•0•0•0•Updated Jun 23, 2025Jun 23, 2025

    • gReLU-applications

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jun 20, 2025Jun 20, 2025

    • PepMapViz

      Public
      R
      •
      Other
      •0•0•0•0•Updated Jun 18, 2025Jun 18, 2025

    • Islander

      Public
      Jupyter Notebook
      •
      MIT License
      •23•119•0•0•Updated Jun 15, 2025Jun 15, 2025

    • spex

      Public
      Jupyter Notebook
      •
      Other
      •0•0•1•0•Updated Jun 13, 2025Jun 13, 2025

    • LNPseqR

      Public
      R
      •
      Other
      •0•0•0•0•Updated Jun 10, 2025Jun 10, 2025

    • PRESAGE

      Public
      Python
      •
      Other
      •1•4•1•0•Updated Jun 9, 2025Jun 9, 2025

    • topological_PRM_for_lungHRCT

      Public
      Lung image analysis pipeline for topological PRM maps
      topological-data-analysislungcopdminkowski-functionalshrctparametric-response-mapping
      Python
      •
      Apache License 2.0
      •0•2•0•0•Updated May 18, 2025May 18, 2025

    • psborrow2

      Public
      psborrow2: Bayesian Dynamic Borrowing Simulation Study and Analysis
      simulation-studybayesian-dynamic-borrowingpsborrow2r
      R
      •
      Other
      •2•19•6•1•Updated May 7, 2025May 7, 2025

    • decima-applications

      Public
      Jupyter Notebook
      •
      Other
      •1•7•0•0•Updated May 1, 2025May 1, 2025

    • pascient

      Public
      Jupyter Notebook
      •
      Other
      •4•16•0•0•Updated Apr 30, 2025Apr 30, 2025

    • spex_spatial_transcriptomics

      Public
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Apr 26, 2025Apr 26, 2025

    • molcap-arena

      Public
      Associated Repository for "MolCap-Arena: A Comprehensive Captioning Benchmark on Language-Enhanced Molecular Property Prediction"
      Python
      •
      Other
      •0•6•0•0•Updated Apr 23, 2025Apr 23, 2025

    • spex_segmentation

      Public
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated Apr 17, 2025Apr 17, 2025

    • Firmament

      Public
      Provides method to perform gene signature search
      Python
      •
      MIT License
      •0•1•0•0•Updated Apr 15, 2025Apr 15, 2025