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    126 repositories

    • glass-box-umap

      Public
      Python package for making UMAP interpretable with exact feature contributions
      Python
      •
      MIT License
      •0•2•0•1•Updated Apr 22, 2026Apr 22, 2026

    • 2026-organism-tractability

      Public archive
      Code for aggregating data on community activity, infrastructure, tooling, throughput, and logistics for research organisms.
      Python
      •
      MIT License
      •1•1•0•0•Updated Apr 15, 2026Apr 15, 2026

    • 2024-chlamy-mutant-motility-pub

      Public
      Collection of data, code, scripts, and notebooks accompanying the pub "Rescuing Chlamydomonas Motility in Mutants Modeling Spermatogenic Failure."
      Jupyter Notebook
      •
      MIT License
      •0•0•2•0•Updated Apr 14, 2026Apr 14, 2026

    • ramanalysis

      Public
      Package for loading and processing spectral data from Arcadia's Raman spectroscopy instruments.
      Python
      •
      MIT License
      •0•2•0•0•Updated Apr 14, 2026Apr 14, 2026

    • 2025-g-p-atlas

      Public
      Repository for the initial G-P atlas pub that presents the model architecture and initial analyses
      Python
      •
      MIT License
      •1•1•0•0•Updated Apr 11, 2026Apr 11, 2026

    • 2024-auto-openraman

      Public
      Python package for automation and extension of OpenRaman
      Python
      •
      MIT License
      •1•7•10•0•Updated Apr 10, 2026Apr 10, 2026

    • 2024-sensory-neuroimaging

      Public
      Data analysis scripts and notebooks for the translation pilot "Label-free neuroimaging in mice captures sensory activity in response to tactile stimuli and acut…
      Python
      •
      MIT License
      •0•0•1•0•Updated Apr 10, 2026Apr 10, 2026

    • arcadia-pycolor

      Public
      Python package for styling plots according to Arcadia's style guide
      plotlymatplotlib
      plotlymatplotlib
      Python
      •
      MIT License
      •0•6•12•0•Updated Apr 9, 2026Apr 9, 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 Apr 8, 2026Apr 8, 2026

    • 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 Apr 8, 2026Apr 8, 2026

    • 2024-ProteinCartography-dCK-validation

      Public
      Python
      •
      MIT License
      •0•0•2•1•Updated Apr 8, 2026Apr 8, 2026

    • 2024-protein-universe

      Public
      R
      •
      MIT License
      •0•1•0•0•Updated Apr 8, 2026Apr 8, 2026

    • PrxteinMPNN

      Public
      functional implementation of ProteinMPNN
      Python
      •
      MIT License
      •1•0•0•0•Updated Apr 7, 2026Apr 7, 2026

    • tandem-domain-proteins

      Public
      Repo containing all code and data for https://doi.org/10.57844/arcadia-2u60-81sg
      HTML
      •
      MIT License
      •0•0•0•0•Updated Apr 2, 2026Apr 2, 2026

    • SurfDock

      Public
      SurfDock is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein-ligand Complex Prediction
      Python
      •
      MIT License
      •31•0•0•0•Updated Apr 2, 2026Apr 2, 2026

    • raman-batch-effects-yeast

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 31, 2026Mar 31, 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•24•20•1•Updated Mar 30, 2026Mar 30, 2026

    • raman-protein-analysis

      Public
      Python codebase for generating figures in the 2026 Arcadia Science pub titled "Spontaneous Raman spectroscopy detects chemical perturbation of protein structure…
      HTML
      •
      MIT License
      •0•0•0•0•Updated Mar 27, 2026Mar 27, 2026

    • readlif

      Public archive
      Leica Image Format (LIF) file reader for Python
      Python
      •
      GNU General Public License v3.0
      •14•38•20•2•Updated Mar 26, 2026Mar 26, 2026

    • arcadia-microscopy-tools

      Public
      High-throughput microscopy image analysis toolkit
      Python
      •
      MIT License
      •1•1•1•0•Updated Mar 23, 2026Mar 23, 2026

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

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 10, 2026Mar 10, 2026

    • 2025_genopheno_local_linear_mapping

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Mar 10, 2026Mar 10, 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 Mar 10, 2026Mar 10, 2026

    • 2025-geno-pheno-attention

      Public
      Jupyter Notebook
      •
      MIT License
      •3•0•0•0•Updated Mar 10, 2026Mar 10, 2026

    • glass-box-umap-notebook-pub

      Public
      Exact feature attribution with UMAP
      Jupyter Notebook
      •
      MIT License
      •3•15•1•0•Updated Mar 10, 2026Mar 10, 2026

    • arcadiathemeR

      Public
      Package for creating ggplot style plots in R that adhere to Arcadia Science style guidelines
      R
      •
      Other
      •0•1•11•0•Updated Feb 26, 2026Feb 26, 2026

    • 2026-scerevisiae-dataset

      Public
      Code for dataset pub on S. cerevisiae
      Python
      •
      MIT License
      •0•0•1•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-raman-spectrometer-comparison

      Public
      Repo for the notebook pub "Comparison of spontaneous Raman spectrometers"
      Jupyter Notebook
      •
      MIT License
      •1•0•2•0•Updated Feb 23, 2026Feb 23, 2026
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