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    37 repositories

    • cell-eval

      Public
      Comprehensive suite for evaluating perturbation prediction models
      Python
      •
      MIT License
      •49•148•7•7•Updated Jul 27, 2026Jul 27, 2026

    • scBaseCount_analysis

      Public
      Data analysis for the scBaseCount manuscript
      Jupyter Notebook
      •0•7•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•34•0•0•Updated Jul 24, 2026Jul 24, 2026

    • SRAgent

      Public
      LLM agents for working with the SRA and associated bioinformatics databases.
      Python
      •
      MIT License
      •35•177•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
      •159•626•36•23•Updated Jul 24, 2026Jul 24, 2026

    • bqtools

      Public
      A command line utilty for working with BINSEQ files
      Rust
      •3•39•5•0•Updated Jul 23, 2026Jul 23, 2026

    • binseq

      Public
      A high efficiency binary format for sequencing data
      Rust
      •7•104•6•0•Updated Jul 20, 2026Jul 20, 2026

    • cell-load

      Public
      pytorch dataloaders for single-cell perturbation data
      Python
      •
      MIT License
      •26•49•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

    • pdex

      Public
      parallel differential expression for single-cell perturbation sequencing
      Python
      •
      MIT License
      •11•25•3•2•Updated Jul 14, 2026Jul 14, 2026

    • numba-mwu

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

    • cyto

      Public
      A mapper for 10x-flex single cell sequencing reads with fixed abstract geometries
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •3•46•11•2•Updated Jul 8, 2026Jul 8, 2026

    • arc-virtual-cell-atlas

      Public
      Arc Virtual Cell Atlas
      Jupyter Notebook
      •57•565•1•0•Updated Jul 1, 2026Jul 1, 2026

    • state-reproduce

      Public
      Reproduce analyses and baselines from the State paper
      Jupyter Notebook
      •6•16•3•0•Updated Jun 29, 2026Jun 29, 2026

    • pycyto

      Public
      python utilities for cyto
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•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
      •519•4k•51•1•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

    • 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
      •311•2•0•0•Updated Jun 17, 2026Jun 17, 2026

    • xsra

      Public
      An efficient CLI to extract sequences from the SRA
      Rust
      •12•124•8•0•Updated Jun 12, 2026Jun 12, 2026

    • Lizard-Wizard

      Public
      Calcium imaging analysis Nextflow pipeline for the Arc Institute
      Python
      •
      MIT License
      •0•5•0•0•Updated May 30, 2026May 30, 2026

    • state-tpu

      Public
      State is a machine learning model that predicts cellular perturbation response across diverse contexts
      Python
      •
      Other
      •159•0•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
      •9.7k•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
      •17•142•1•0•Updated Apr 28, 2026Apr 28, 2026

    • brain-agent-template

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

    • ScreenPro2

      Public
      Flexible analysis of high-content CRISPR screening
      crispr-analysiscrisprphenotypes
      crispr-analysiscrisprphenotypescrispr-cas9functional-genomicsngs-analysisperturbation-screensequencing-datacrispr-cas12
      Python
      •
      Other
      •7•33•12•0•Updated Mar 6, 2026Mar 6, 2026

    • MULTI-evolve

      Public
      MULTI-evolve: a machine learning-guided end-to-end framework for engineering hyperactive multi-mutant proteins
      Python
      •
      Apache License 2.0
      •35•84•0•0•Updated Feb 27, 2026Feb 27, 2026

    • ncbi-vdb-sys

      Public
      Rust bindings to NCBI-VDB to interact with SRA files programmatically
      Rust
      •2•6•1•0•Updated Jan 30, 2026Jan 30, 2026

    • mmr

      Public
      A minimap2 implementation with binseq inputs
      Rust
      •0•18•0•0•Updated Dec 11, 2025Dec 11, 2025

    • cell-filter

      Public
      A python implementation of the EmptyDrops algorithm
      Python
      •
      MIT License
      •0•2•0•0•Updated Nov 13, 2025Nov 13, 2025

    • kmer-count

      Public
      A simple utility used to count kmers
      Rust
      •0•1•0•0•Updated Oct 24, 2025Oct 24, 2025
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