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    • xsra

      Public
      An efficient CLI to extract sequences from the SRA
      Rust
      1212380Updated Jun 12, 2026Jun 12, 2026
    • Calcium imaging analysis pipeline of outputs from Lizard-Wizard for the Arc Institute.
      Python
      MIT License
      0100Updated Jun 11, 2026Jun 11, 2026
    • Arc Virtual Cell Atlas
      Jupyter Notebook
      5253710Updated Jun 10, 2026Jun 10, 2026
    • cell-eval

      Public
      Comprehensive suite for evaluating perturbation prediction models
      Python
      MIT License
      4813777Updated Jun 9, 2026Jun 9, 2026
    • pdex

      Public
      parallel differential expression for single-cell perturbation sequencing
      Python
      MIT License
      112533Updated Jun 1, 2026Jun 1, 2026
    • Calcium imaging analysis Nextflow pipeline for the Arc Institute
      Python
      MIT License
      0400Updated 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
      245100Updated May 22, 2026May 22, 2026
    • SRAgent

      Public
      LLM agents for working with the SRA and associated bioinformatics databases.
      Python
      MIT License
      3417431Updated May 22, 2026May 22, 2026
    • state-tpu

      Public
      State is a machine learning model that predicts cellular perturbation response across diverse contexts
      Python
      Other
      156000Updated May 8, 2026May 8, 2026
    • 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
      300200Updated May 7, 2026May 7, 2026
    • fastapi

      Public
      FastAPI framework, high performance, easy to learn, fast to code, ready for production
      Python
      MIT License
      9.4k000Updated May 6, 2026May 6, 2026
    • binseq

      Public
      A high efficiency binary format for sequencing data
      Rust
      610270Updated May 5, 2026May 5, 2026
    • state

      Public
      State is a machine learning model that predicts cellular perturbation response across diverse contexts
      Python
      Other
      1565943523Updated 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
      1713710Updated Apr 28, 2026Apr 28, 2026
    • cell-load

      Public
      pytorch dataloaders for single-cell perturbation data
      Python
      MIT License
      2645126Updated Apr 24, 2026Apr 24, 2026
    • brain-agent-template

      Public template
      Template for autonomous self-evolving Claude Code brain agents
      0100Updated Apr 18, 2026Apr 18, 2026
    • bqtools

      Public
      A command line utilty for working with BINSEQ files
      Rust
      33880Updated Mar 31, 2026Mar 31, 2026
    • evo2

      Public
      Genome modeling and design across all domains of life
      Jupyter Notebook
      Apache License 2.0
      5013.9k521Updated Mar 20, 2026Mar 20, 2026
    • Flexible analysis of high-content CRISPR screening
      Python
      Other
      732120Updated Mar 6, 2026Mar 6, 2026
    • MULTI-evolve: a machine learning-guided end-to-end framework for engineering hyperactive multi-mutant proteins
      Python
      Apache License 2.0
      348300Updated Feb 27, 2026Feb 27, 2026
    • numba-mwu

      Public
      Python
      0100Updated Feb 25, 2026Feb 25, 2026
    • Reproduce analyses and baselines from the State paper
      Jupyter Notebook
      61530Updated Feb 25, 2026Feb 25, 2026
    • pycyto

      Public
      python utilities for cyto
      Python
      BSD 3-Clause "New" or "Revised" License
      1151Updated Feb 12, 2026Feb 12, 2026
    • Data analysis for the scBaseCount manuscript
      Jupyter Notebook
      0700Updated Feb 9, 2026Feb 9, 2026
    • Rust bindings to NCBI-VDB to interact with SRA files programmatically
      Rust
      2610Updated Jan 30, 2026Jan 30, 2026
    • mmr

      Public
      A minimap2 implementation with binseq inputs
      Rust
      01800Updated Dec 11, 2025Dec 11, 2025
    • A python implementation of the EmptyDrops algorithm
      Python
      MIT License
      0200Updated Nov 13, 2025Nov 13, 2025
    • A simple utility used to count kmers
      Rust
      0100Updated Oct 24, 2025Oct 24, 2025
    • A command line and web interface for designing Bridge RNAs for Bridge Editing.
      Python
      MIT License
      1100Updated Sep 25, 2025Sep 25, 2025
    • BioNeMo Framework: For building and adapting AI models in drug discovery at scale
      Jupyter Notebook
      158100Updated Sep 17, 2025Sep 17, 2025
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