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    162 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
      •1•11•2•3•Updated Aug 21, 2026Aug 21, 2026

    • rdborrow

      Public
      External Control Borrowing for Rare Disease Simulation and Analysis
      R
      •
      Other
      •0•0•6•2•Updated Aug 20, 2026Aug 20, 2026

    • DuckDBGRanges

      Public
      R
      •
      Other
      •0•0•0•0•Updated Aug 20, 2026Aug 20, 2026

    • DuckDBSpatial

      Public
      R
      •
      Other
      •0•2•0•0•Updated Aug 19, 2026Aug 19, 2026

    • DuckDBDataFrame

      Public
      R
      •
      Other
      •1•1•1•1•Updated Aug 19, 2026Aug 19, 2026

    • jmpost

      Public
      R
      •4•17•31•0•Updated Aug 19, 2026Aug 19, 2026

    • PerturbME

      Public
      Analysis code for Perturb-ME: scalable mechanism discovery from phenotype-enriched genome-wide CRISPR screens (Wang, Gu, Frangieh et al., bioRxiv 2026)
      single-cellfunctional-genomicsmelanoma
      single-cellfunctional-genomicsmelanomacite-seqcrispr-screenperturb-seqmhc-class-i
      Python
      •
      MIT License
      •0•1•0•0•Updated Aug 18, 2026Aug 18, 2026

    • DuckDBArray

      Public
      R
      •
      Other
      •0•0•0•0•Updated Aug 13, 2026Aug 13, 2026

    • MultiAssaySpatialExperiment

      Public
      R
      •
      Other
      •0•0•0•0•Updated Aug 12, 2026Aug 12, 2026

    • checked

      Public
      batch R CMD check management
      rchecksrevdeps
      rchecksrevdeps
      R
      •
      Other
      •2•9•15•0•Updated Aug 10, 2026Aug 10, 2026

    • BiocDuckDB

      Public
      R
      •
      Other
      •0•2•0•0•Updated Aug 9, 2026Aug 9, 2026

    • cna_star

      Public
      Python
      •0•1•0•0•Updated Aug 4, 2026Aug 4, 2026

    • sceps

      Public
      scEPS integrates GWAS and single-cell disease cell atlas data to identify disease-associated cell neighborhoods.
      geneticssingle-cellgwas-summary-statistics
      geneticssingle-cellgwas-summary-statisticscomplex-diseases
      Python
      •
      MIT License
      •0•3•0•0•Updated Aug 4, 2026Aug 4, 2026

    • sceps_manuscript

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Aug 4, 2026Aug 4, 2026

    • gmap-gsnap

      Public
      Programs for aligning long and short RNA-seq and DNA-seq reads to genomes
      C
      •
      Other
      •0•1•0•0•Updated Aug 3, 2026Aug 3, 2026

    • covtracer

      Public
      Tools for contextualizing tests, built using covr test traces.
      R
      •
      Other
      •4•23•10•0•Updated Jul 27, 2026Jul 27, 2026

    • AssayBench

      Public
      AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents
      benchmarkmetricsbiology
      benchmarkmetricsbiologyscreencrisprllms
      Python
      •
      MIT License
      •0•12•0•0•Updated Jul 24, 2026Jul 24, 2026

    • BioReasoningChallenge

      Public
      MLGenX BioReasoning Challenge 2026
      Python
      •6•13•0•0•Updated Jul 22, 2026Jul 22, 2026

    • nfnull

      Public
      Jupyter Notebook
      •
      MIT License
      •1•2•0•0•Updated Jul 15, 2026Jul 15, 2026

    • perturbmatch_analysis

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Jul 11, 2026Jul 11, 2026

    • perturbmatch

      Public
      R
      •
      Other
      •0•6•0•0•Updated Jul 11, 2026Jul 11, 2026

    • sp_pipeline_public

      Public
      Python
      •
      MIT License
      •0•2•0•0•Updated Jul 7, 2026Jul 7, 2026

    • SpatialQPFs

      Public
      R
      •0•6•0•0•Updated Jul 3, 2026Jul 3, 2026

    • BayesERtools

      Public
      R
      •
      Other
      •4•7•4•0•Updated Jun 30, 2026Jun 30, 2026

    • BayesERbook

      Public
      R
      •
      Other
      •1•4•1•1•Updated Jun 30, 2026Jun 30, 2026

    • inSeqAPI_Offline

      Public
      C#
      •
      MIT License
      •0•2•0•0•Updated Jun 23, 2026Jun 23, 2026

    • gReLU

      Public
      gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
      Python
      •
      MIT License
      •57•362•20•4•Updated Jun 12, 2026Jun 12, 2026

    • sceps_sim

      Public
      Python
      •0•0•0•0•Updated Jun 11, 2026Jun 11, 2026

    • decima

      Public
      Decima is a Python library to train sequence models on single-cell RNA-seq data.
      Python
      •
      Other
      •9•80•2•1•Updated Jun 4, 2026Jun 4, 2026

    • semantic-transport-generation

      Public
      Python
      •
      MIT License
      •0•7•0•0•Updated Jun 3, 2026Jun 3, 2026
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