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@Arcadia-Science

Arcadia Science

README.md

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Welcome to @Arcadia-Science!

At Arcadia, one of our central tenets is that our science should be maximally useful. Computational tasks are embedded in all aspects of our scientific inquiry, so we need our computing strategies to be maximally useful too. What does this mean? In addition to aligning with scientific priorities across Arcadia, we believe that useful computing is ✨ innovative, 👩‍💻usable, 🔁 reproducible.

Popular repositories Loading

  1. ProteinCartography ProteinCartography Public

    A pipeline to build similarity maps of protein space

    Jupyter Notebook 42 12

  2. readlif readlif Public

    Leica Image Format (LIF) file reader for Python

    Python 38 14

  3. metagenomics metagenomics Public

    A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies

    Nextflow 38 5

  4. seqqc seqqc Public

    A Nextflow pipeline to identify quality control issues with new sequencing data.

    Groovy 29

  5. sourmashconsumr sourmashconsumr Public

    Working with the outputs of sourmash in R

    Standard ML 28 4

  6. noveltree noveltree Public

    NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.

    Nextflow 23 5

Repositories

Showing 10 of 121 repositories
  • arcadia-microscopy-tools Public

    High-throughput microscopy image analysis toolkit

    Arcadia-Science/arcadia-microscopy-tools’s past year of commit activity
    Python 1 MIT 1 1 0 Updated Feb 28, 2026
  • arcadia-pycolor Public

    Python package for styling plots according to Arcadia's style guide

    Arcadia-Science/arcadia-pycolor’s past year of commit activity
    Python 7 MIT 0 12 (1 issue needs help) 0 Updated Feb 26, 2026
  • glass-box-umap Public

    Python package for making UMAP interpretable with exact feature contributions

    Arcadia-Science/glass-box-umap’s past year of commit activity
    Python 1 MIT 0 0 1 Updated Feb 26, 2026
  • arcadiathemeR Public

    Package for creating ggplot style plots in R that adhere to Arcadia Science style guidelines

    Arcadia-Science/arcadiathemeR’s past year of commit activity
    R 1 0 11 0 Updated Feb 26, 2026
  • 2026-scerevisiae-dataset Public

    Code for dataset pub on S. cerevisiae

    Arcadia-Science/2026-scerevisiae-dataset’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Feb 23, 2026
  • 2025-geno-pheno-attention Public
    Arcadia-Science/2025-geno-pheno-attention’s past year of commit activity
    Jupyter Notebook 0 MIT 3 0 0 Updated Feb 23, 2026
  • notebook-pub-template Public template
    Arcadia-Science/notebook-pub-template’s past year of commit activity
    Lua 9 MIT 2 4 0 Updated Feb 23, 2026
  • notebook-pub-test Public Forked from Arcadia-Science/2025-raman-spectrometer-comparison

    A test notebook pub

    Arcadia-Science/notebook-pub-test’s past year of commit activity
    Jupyter Notebook 0 MIT 1 0 0 Updated Feb 23, 2026
  • 2025-phylogenetic-analysis-of-msa-pairformer Public
    Arcadia-Science/2025-phylogenetic-analysis-of-msa-pairformer’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Feb 23, 2026
  • 2025-glass-box-umap-notebook-pub Public

    Exact feature attribution with UMAP

    Arcadia-Science/2025-glass-box-umap-notebook-pub’s past year of commit activity
    Jupyter Notebook 13 MIT 2 1 0 Updated Feb 23, 2026
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