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Arc Research Institute

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  1. evo2 evo2 Public

    Genome modeling and design across all domains of life

    Jupyter Notebook 3.3k 384

  2. state state Public

    State is a machine learning model that predicts cellular perturbation response across diverse contexts

    Python 502 142

  3. arc-virtual-cell-atlas arc-virtual-cell-atlas Public

    Arc Virtual Cell Atlas

    Jupyter Notebook 486 48

  4. SRAgent SRAgent Public

    LLM agents for working with the SRA and associated bioinformatics databases.

    Python 143 30

  5. xsra xsra Public

    An efficient CLI to extract sequences from the SRA

    Rust 119 10

  6. cell-eval cell-eval Public

    Comprehensive suite for evaluating perturbation prediction models

    Python 118 42

Repositories

Showing 10 of 29 repositories
  • binseq Public

    A high efficiency binary format for sequencing data

    ArcInstitute/binseq’s past year of commit activity
    Rust 91 5 8 0 Updated Jan 22, 2026
  • Wizards-Staff Public

    Calcium imaging analysis pipeline of outputs from Lizard-Wizard for the Arc Institute.

    ArcInstitute/Wizards-Staff’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Jan 21, 2026
  • state Public

    State is a machine learning model that predicts cellular perturbation response across diverse contexts

    ArcInstitute/state’s past year of commit activity
    Python 502 142 47 (1 issue needs help) 20 Updated Jan 21, 2026
  • cell-eval Public

    Comprehensive suite for evaluating perturbation prediction models

    ArcInstitute/cell-eval’s past year of commit activity
    Python 118 MIT 42 3 6 Updated Jan 17, 2026
  • stack Public

    Stack is a single-cell foundation model that enables in-context learning at inference time.

    ArcInstitute/stack’s past year of commit activity
    Jupyter Notebook 68 6 0 0 Updated Jan 10, 2026
  • bqtools Public

    A command line utilty for working with BINSEQ files

    ArcInstitute/bqtools’s past year of commit activity
    Rust 33 3 7 0 Updated Jan 7, 2026
  • pdex Public

    parallel differential expression for single-cell perturbation sequencing

    ArcInstitute/pdex’s past year of commit activity
    Python 24 MIT 7 8 2 Updated Jan 7, 2026
  • arc-virtual-cell-atlas Public

    Arc Virtual Cell Atlas

    ArcInstitute/arc-virtual-cell-atlas’s past year of commit activity
    Jupyter Notebook 486 48 6 0 Updated Dec 18, 2025
  • Lizard-Wizard Public

    Calcium imaging analysis Nextflow pipeline for the Arc Institute

    ArcInstitute/Lizard-Wizard’s past year of commit activity
    Python 2 MIT 0 0 0 Updated Dec 17, 2025
  • mmr Public

    A minimap2 implementation with binseq inputs

    ArcInstitute/mmr’s past year of commit activity
    Rust 17 0 0 0 Updated Dec 11, 2025

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