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    25 repositories

    • state

      Public
      State is a machine learning model that predicts cellular perturbation response across diverse contexts
      Python
      •
      Other
      •69•308•28•12•Updated Aug 8, 2025Aug 8, 2025

    • cell-eval

      Public
      Comprehensive suite for evaluating perturbation prediction models
      Python
      •
      MIT License
      •21•66•5•1•Updated Aug 6, 2025Aug 6, 2025

    • bqtools

      Public
      A command line utilty for working with BINSEQ files
      Rust
      •2•22•7•0•Updated Aug 4, 2025Aug 4, 2025

    • pdex

      Public
      parallel differential expression for single-cell perturbation sequencing
      Python
      •
      MIT License
      •3•12•3•1•Updated Aug 4, 2025Aug 4, 2025

    • cell-load

      Public
      dataloaders for state-sets models
      Python
      •
      MIT License
      •10•15•10•3•Updated Aug 3, 2025Aug 3, 2025

    • xsra

      Public
      An efficient CLI to extract sequences from the SRA
      Rust
      •10•111•4•0•Updated Jul 29, 2025Jul 29, 2025

    • mmr

      Public
      A minimap2 implementation with binseq inputs
      Rust
      •0•15•1•0•Updated Jul 29, 2025Jul 29, 2025

    • evo2

      Public
      Genome modeling and design across all domains of life
      Jupyter Notebook
      •
      Apache License 2.0
      •327•3k•26•1•Updated Jul 23, 2025Jul 23, 2025

    • Lizard-Wizard

      Public
      Calcium imaging analysis Nextflow pipeline for the Arc Institute
      Python
      •
      MIT License
      •0•2•0•0•Updated Jul 18, 2025Jul 18, 2025

    • SRAgent

      Public
      LLM agents for working with the SRA and associated bioinformatics databases.
      Python
      •
      MIT License
      •25•110•2•1•Updated Jul 18, 2025Jul 18, 2025

    • scRecounter

      Public
      Nextflow pipeline to re-process all public single-cell RNA-seq data
      Jupyter Notebook
      •
      MIT License
      •3•29•0•0•Updated Jul 9, 2025Jul 9, 2025

    • binseq

      Public
      A high efficiency binary format for sequencing data
      Rust
      •5•68•4•0•Updated Jul 1, 2025Jul 1, 2025

    • state-reproduce

      Public
      Reproduce analyses and baselines from the State paper
      Jupyter Notebook
      •2•4•0•0•Updated Jun 23, 2025Jun 23, 2025

    • ncbi-vdb-sys

      Public
      Rust bindings to NCBI-VDB to interact with SRA files programmatically
      Rust
      •1•5•1•0•Updated May 9, 2025May 9, 2025

    • arc-virtual-cell-atlas

      Public
      Arc Virtual Cell Atlas
      Jupyter Notebook
      •37•393•6•0•Updated May 6, 2025May 6, 2025

    • binseq-bindings

      Public
      C and C++ Bindings to the BINSEQ library
      Rust
      •2•0•0•1•Updated May 2, 2025May 2, 2025

    • vbinseq

      Public archive
      [ARCHIVED] An extension of BINSEQ to handle variable-length records - See main binseq repo
      Rust
      •0•6•0•0•Updated Apr 23, 2025Apr 23, 2025

    • kmer-count

      Public
      A simple utility used to count kmers
      Rust
      •0•0•0•0•Updated Apr 8, 2025Apr 8, 2025

    • ScreenPro2

      Public
      Flexible analysis of high-content CRISPR screening
      crispr-analysiscrisprphenotypescrispr-cas9functional-genomicsngs-analysisperturbation-screensequencing-datacrispr-cas12
      Python
      •
      Other
      •6•31•12•0•Updated Apr 7, 2025Apr 7, 2025

    • Wizards-Staff

      Public
      Calcium imaging analysis pipeline of outputs from Lizard-Wizard for the Arc Institute.
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 21, 2025Mar 21, 2025

    • scBaseCamp_analysis

      Public
      Analysis of scBaseCamp data
      Jupyter Notebook
      •0•0•0•0•Updated Feb 27, 2025Feb 27, 2025

    • 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
      •228•1•0•0•Updated Dec 26, 2024Dec 26, 2024

    • InVivoMultimodalPerturbation

      Public
      Python
      •1•0•0•0•Updated Aug 29, 2024Aug 29, 2024

    • bridge-rna-designer

      Public
      A command line and web interface for designing Bridge RNAs for Bridge Editing.
      Python
      •
      MIT License
      •0•1•0•0•Updated Aug 25, 2024Aug 25, 2024

    • RNAtargeting_web_custom

      Public
      source code of the custom page for the RNA targeting website - Cas13d guide design
      C
      •
      MIT License
      •0•5•1•0•Updated Mar 7, 2024Mar 7, 2024