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    42 repositories

    • cell-eval2

      Public
      GPU-accelerated evaluation of perturbation prediction models
      Python
      •
      MIT License
      •4•32•0•0•Updated Oct 16, 2026Oct 16, 2026

    • cyto

      Public
      A mapper for 10x-flex single cell sequencing reads with fixed abstract geometries
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •4•50•10•1•Updated Oct 14, 2026Oct 14, 2026

    • arc-cluster-toolkit

      Public
      Cluster Toolkit is an open-source software offered by Google Cloud which makes it easy for customers to deploy AI/ML and HPC environments on Google Cloud.
      HCL
      •
      Apache License 2.0
      •329•2•0•0•Updated Oct 9, 2026Oct 9, 2026

    • Lizard-Wizard

      Public
      Calcium imaging analysis Nextflow pipeline for the Arc Institute
      Python
      •
      MIT License
      •0•5•1•0•Updated Oct 6, 2026Oct 6, 2026

    • pie

      Public
      PIE is a perturbation effect prediction model that generalizes to unseen biological conditions
      Python
      •
      Other
      •5•55•0•0•Updated Oct 5, 2026Oct 5, 2026

    • arc-virtual-cell-atlas

      Public
      Arc Virtual Cell Atlas
      Jupyter Notebook
      •66•632•3•1•Updated Sep 29, 2026Sep 29, 2026

    • scx

      Public archive
      A purpose-built binary file format for single-cell RNA-seq data
      Rust
      •
      MIT License
      •1•0•0•0•Updated Sep 24, 2026Sep 24, 2026

    • bqtools

      Public
      A command line utilty for working with BINSEQ files
      Rust
      •
      MIT License
      •3•51•7•0•Updated Sep 23, 2026Sep 23, 2026

    • ScreenPro2

      Public
      Flexible analysis of high-content CRISPR screening
      crispr-analysiscrisprphenotypes
      crispr-analysiscrisprphenotypescrispr-cas9functional-genomicsngs-analysisperturbation-screensequencing-datacrispr-cas12
      Python
      •
      Other
      •7•34•13•0•Updated Sep 14, 2026Sep 14, 2026

    • cellstream

      Public
      Compressed per-cell storage for large single-cell AnnData, built for scattered random access
      Python
      •
      MIT License
      •0•2•1•0•Updated Sep 4, 2026Sep 4, 2026

    • binseq

      Public
      A high efficiency binary format for sequencing data
      Rust
      •9•110•6•1•Updated Aug 26, 2026Aug 26, 2026

    • pdex

      Public
      parallel differential expression for single-cell perturbation sequencing
      Python
      •
      MIT License
      •11•31•3•2•Updated Aug 26, 2026Aug 26, 2026

    • gpudge

      Public
      Lightweight GPU-only Mann–Whitney U differential expression for single-cell CRISPR perturbation screens
      pythonbioinformaticsgpu
      pythonbioinformaticsgpucudacrisprsingle-celldifferential-expressionmann-whitneywilcoxonperturbation-screen
      Python
      •
      MIT License
      •0•7•0•0•Updated Aug 20, 2026Aug 20, 2026

    • cell-eval

      Public
      Comprehensive suite for evaluating perturbation prediction models
      Python
      •
      MIT License
      •52•164•7•7•Updated Jul 27, 2026Jul 27, 2026

    • scBaseCount_analysis

      Public
      Data analysis for the scBaseCount manuscript
      Jupyter Notebook
      •1•15•0•0•Updated Jul 24, 2026Jul 24, 2026

    • scRecounter

      Public
      Nextflow pipeline to re-process all public single-cell RNA-seq data
      Jupyter Notebook
      •
      MIT License
      •3•39•0•0•Updated Jul 24, 2026Jul 24, 2026

    • SRAgent

      Public
      LLM agents for working with the SRA and associated bioinformatics databases.
      Python
      •
      MIT License
      •37•195•3•0•Updated Jul 24, 2026Jul 24, 2026

    • state

      Public
      State is a machine learning model that predicts cellular perturbation response across diverse contexts
      Python
      •
      Other
      •168•728•41•21•Updated Jul 24, 2026Jul 24, 2026

    • cell-load

      Public
      pytorch dataloaders for single-cell perturbation data
      Python
      •
      MIT License
      •28•55•12•5•Updated Jul 18, 2026Jul 18, 2026

    • bioconcord

      Public
      A systematic evaluation framework for benchmarking the degree of concordance between biological conclusions inferred from simulated perturbation datasets and th…
      Python
      •
      MIT License
      •0•2•0•0•Updated Jul 15, 2026Jul 15, 2026

    • numba-mwu

      Public
      Python
      •0•1•1•0•Updated Jul 14, 2026Jul 14, 2026

    • state-reproduce

      Public
      Reproduce analyses and baselines from the State paper
      Jupyter Notebook
      •6•18•3•0•Updated Jun 29, 2026Jun 29, 2026

    • pycyto

      Public
      python utilities for cyto
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•4•0•Updated Jun 26, 2026Jun 26, 2026

    • evo2

      Public
      Genome modeling and design across all domains of life
      Jupyter Notebook
      •
      Apache License 2.0
      •571•4.3k•54•2•Updated Jun 19, 2026Jun 19, 2026

    • Wizards-Staff

      Public
      Calcium imaging analysis pipeline of outputs from Lizard-Wizard for the Arc Institute.
      Python
      •
      MIT License
      •0•1•1•0•Updated Jun 17, 2026Jun 17, 2026

    • xsra

      Public
      An efficient CLI to extract sequences from the SRA
      Rust
      •12•132•8•0•Updated Jun 12, 2026Jun 12, 2026

    • state-tpu

      Public
      State is a machine learning model that predicts cellular perturbation response across diverse contexts
      Python
      •
      Other
      •168•1•0•0•Updated May 8, 2026May 8, 2026

    • fastapi

      Public
      FastAPI framework, high performance, easy to learn, fast to code, ready for production
      Python
      •
      MIT License
      •10k•0•0•0•Updated May 6, 2026May 6, 2026

    • stack

      Public
      Stack is a single-cell foundation model that enables in-context learning at inference time.
      Jupyter Notebook
      •
      Other
      •20•168•1•0•Updated Apr 28, 2026Apr 28, 2026

    • brain-agent-template

      Public template
      Template for autonomous self-evolving Claude Code brain agents
      1•2•0•0•Updated Apr 18, 2026Apr 18, 2026
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