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    36 repositories

    • xsra

      Public
      An efficient CLI to extract sequences from the SRA
      Rust
      •12•123•8•0•Updated Jun 12, 2026Jun 12, 2026

    • Wizards-Staff

      Public
      Calcium imaging analysis pipeline of outputs from Lizard-Wizard for the Arc Institute.
      Python
      •
      MIT License
      •0•1•0•0•Updated Jun 11, 2026Jun 11, 2026

    • arc-virtual-cell-atlas

      Public
      Arc Virtual Cell Atlas
      Jupyter Notebook
      •52•537•1•0•Updated Jun 10, 2026Jun 10, 2026

    • cell-eval

      Public
      Comprehensive suite for evaluating perturbation prediction models
      Python
      •
      MIT License
      •48•137•7•7•Updated Jun 9, 2026Jun 9, 2026

    • pdex

      Public
      parallel differential expression for single-cell perturbation sequencing
      Python
      •
      MIT License
      •11•25•3•3•Updated Jun 1, 2026Jun 1, 2026

    • Lizard-Wizard

      Public
      Calcium imaging analysis Nextflow pipeline for the Arc Institute
      Python
      •
      MIT License
      •0•4•0•0•Updated May 30, 2026May 30, 2026

    • cyto

      Public
      A mapper for 10x-flex single cell sequencing reads with fixed abstract geometries
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •2•45•10•0•Updated May 22, 2026May 22, 2026

    • SRAgent

      Public
      LLM agents for working with the SRA and associated bioinformatics databases.
      Python
      •
      MIT License
      •34•174•3•1•Updated May 22, 2026May 22, 2026

    • state-tpu

      Public
      State is a machine learning model that predicts cellular perturbation response across diverse contexts
      Python
      •
      Other
      •156•0•0•0•Updated May 8, 2026May 8, 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
      •300•2•0•0•Updated May 7, 2026May 7, 2026

    • fastapi

      Public
      FastAPI framework, high performance, easy to learn, fast to code, ready for production
      Python
      •
      MIT License
      •9.4k•0•0•0•Updated May 6, 2026May 6, 2026

    • binseq

      Public
      A high efficiency binary format for sequencing data
      Rust
      •6•102•7•0•Updated May 5, 2026May 5, 2026

    • state

      Public
      State is a machine learning model that predicts cellular perturbation response across diverse contexts
      Python
      •
      Other
      •156•594•35•23•Updated May 4, 2026May 4, 2026

    • stack

      Public
      Stack is a single-cell foundation model that enables in-context learning at inference time.
      Jupyter Notebook
      •
      Other
      •17•137•1•0•Updated Apr 28, 2026Apr 28, 2026

    • cell-load

      Public
      pytorch dataloaders for single-cell perturbation data
      Python
      •
      MIT License
      •26•45•12•6•Updated Apr 24, 2026Apr 24, 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

    • bqtools

      Public
      A command line utilty for working with BINSEQ files
      Rust
      •3•38•8•0•Updated Mar 31, 2026Mar 31, 2026

    • evo2

      Public
      Genome modeling and design across all domains of life
      Jupyter Notebook
      •
      Apache License 2.0
      •501•3.9k•52•1•Updated Mar 20, 2026Mar 20, 2026

    • ScreenPro2

      Public
      Flexible analysis of high-content CRISPR screening
      crispr-analysiscrisprphenotypes
      crispr-analysiscrisprphenotypescrispr-cas9functional-genomicsngs-analysisperturbation-screensequencing-datacrispr-cas12
      Python
      •
      Other
      •7•32•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
      •34•83•0•0•Updated Feb 27, 2026Feb 27, 2026

    • numba-mwu

      Public
      Python
      •0•1•0•0•Updated Feb 25, 2026Feb 25, 2026

    • state-reproduce

      Public
      Reproduce analyses and baselines from the State paper
      Jupyter Notebook
      •6•15•3•0•Updated Feb 25, 2026Feb 25, 2026

    • pycyto

      Public
      python utilities for cyto
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•5•1•Updated Feb 12, 2026Feb 12, 2026

    • scBaseCount_analysis

      Public
      Data analysis for the scBaseCount manuscript
      Jupyter Notebook
      •0•7•0•0•Updated Feb 9, 2026Feb 9, 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

    • bridge-rna-designer

      Public
      A command line and web interface for designing Bridge RNAs for Bridge Editing.
      Python
      •
      MIT License
      •1•1•0•0•Updated Sep 25, 2025Sep 25, 2025

    • bionemo-framework

      Public
      BioNeMo Framework: For building and adapting AI models in drug discovery at scale
      Jupyter Notebook
      •158•1•0•0•Updated Sep 17, 2025Sep 17, 2025
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