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    121 repositories

    • arcadia-microscopy-tools

      Public
      High-throughput microscopy image analysis toolkit
      Python
      •
      MIT License
      •1•1•1•0•Updated Feb 24, 2026Feb 24, 2026

    • 2026-scerevisiae-dataset

      Public
      Code for dataset pub on S. cerevisiae
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 23, 2026Feb 23, 2026

    • 2025-geno-pheno-attention

      Public
      Jupyter Notebook
      •
      MIT License
      •3•0•0•0•Updated Feb 23, 2026Feb 23, 2026

    • notebook-pub-template

      Public template
      Lua
      •
      MIT License
      •2•9•4•0•Updated Feb 23, 2026Feb 23, 2026

    • notebook-pub-test

      Public
      A test notebook pub
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Feb 23, 2026Feb 23, 2026

    • 2025-phylogenetic-analysis-of-msa-pairformer

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 23, 2026Feb 23, 2026

    • 2025-glass-box-umap-notebook-pub

      Public
      Exact feature attribution with UMAP
      Jupyter Notebook
      •
      MIT License
      •2•13•1•0•Updated Feb 23, 2026Feb 23, 2026

    • 2025-asr-plms

      Public
      Exploring the intersection of Ancestral Sequence Reconstruction, Protein Language Models, and Consensus Bias
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 23, 2026Feb 23, 2026

    • 2025_genopheno_local_linear_mapping

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Feb 23, 2026Feb 23, 2026

    • 2025-raman-spectrometer-comparison

      Public
      Repo for the notebook pub "Comparison of spontaneous Raman spectrometers"
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Feb 23, 2026Feb 23, 2026

    • 2026-arcadia-syntax-highlighting

      Public
      JavaScript
      •0•0•0•0•Updated Feb 23, 2026Feb 23, 2026

    • noveltree

      Public
      NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene fam…
      Nextflow
      •
      GNU Affero General Public License v3.0
      •5•23•19•2•Updated Feb 20, 2026Feb 20, 2026

    • notebook-pub-theme

      Public
      A Quarto extension that provides shared styling and infrastructure for Arcadia Science notebook publications.
      HTML
      •0•0•0•0•Updated Feb 20, 2026Feb 20, 2026

    • glass-box-umap

      Public
      Python package for making UMAP interpretable with exact feature contributions
      Python
      •
      MIT License
      •0•1•0•2•Updated Feb 19, 2026Feb 19, 2026

    • 2026-marine-broth-chlamy

      Public
      Image processing tools for fluorescence microscopy analysis of Chlamydomonas morphological transformations. Associated with "Marine Broth induces extreme morp…
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 13, 2026Feb 13, 2026

    • arcadia-software-handbook

      Public
      Core software engineering guides and policies at Arcadia Science
      Makefile
      •
      Creative Commons Zero v1.0 Universal
      •0•3•0•0•Updated Feb 12, 2026Feb 12, 2026

    • ramanalysis

      Public
      Package for loading and processing spectral data from Arcadia's Raman spectroscopy instruments.
      Python
      •
      MIT License
      •0•3•0•0•Updated Feb 11, 2026Feb 11, 2026

    • 2026-organism-tractability

      Public archive
      Code for aggregating data on community activity, infrastructure, tooling, throughput, and logistics for research organisms.
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 10, 2026Feb 10, 2026

    • 2024-paired-token-masking

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Feb 5, 2026Feb 5, 2026

    • 2026-interactive-figure-search-strategy-bio-utility

      Public
      Python script to generate the figure gallery embedded in the Arcadia Science pub, "Strategizing the search for bio-utility: Establishing a framework for evoluti…
      HTML
      •
      MIT License
      •0•0•0•0•Updated Feb 5, 2026Feb 5, 2026

    • 2026-spombe-dataset

      Public template
      Code for 2026 S. pombe dataset pub
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 4, 2026Feb 4, 2026

    • 2026-prospective-biology

      Public
      R
      •
      MIT License
      •0•1•0•0•Updated Feb 3, 2026Feb 3, 2026

    • sourmashconsumr

      Public
      Working with the outputs of sourmash in R
      sourmash
      Standard ML
      •
      Other
      •4•28•17•1•Updated Jan 15, 2026Jan 15, 2026

    • 2023-nr-clustering

      Public
      Clustering the NCBI nr database with mmseq2 (90% length, 90% identity). Inspired by the NCBI's experimental ClusteredNR database.
      Python
      •
      MIT License
      •2•23•2•0•Updated Nov 7, 2025Nov 7, 2025

    • ProteinCartography

      Public
      A pipeline to build similarity maps of protein space
      Jupyter Notebook
      •
      MIT License
      •12•42•5•0•Updated Oct 17, 2025Oct 17, 2025

    • arcadia-pycolor

      Public
      Python package for styling plots according to Arcadia's style guide
      plotlymatplotlib
      Python
      •
      MIT License
      •0•7•12•0•Updated Oct 7, 2025Oct 7, 2025

    • 2024-publishing-v2-early-assessment

      Public
      Data and code associated with "Early update on Arcadia publishing 2.0: Scientists are in charge, speed is an issue."
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 16, 2025Sep 16, 2025

    • 2025-GFP-variant-design

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 9, 2025Sep 9, 2025

    • 2024-auto-openraman

      Public
      Python package for automation and extension of OpenRaman
      Python
      •
      MIT License
      •1•5•7•0•Updated Sep 8, 2025Sep 8, 2025

    • g-p-atlas

      Public
      Python
      •
      MIT License
      •0•1•1•0•Updated Sep 4, 2025Sep 4, 2025