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@Arcadia-Science

Arcadia Science

README.md

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. Read more about our efforts.

Popular repositories Loading

  1. metagenomics metagenomics Public

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

    Nextflow 37 3

  2. readlif readlif Public

    Leica Image Format (LIF) file reader for Python

    Python 34 13

  3. ProteinCartography ProteinCartography Public

    a pipeline to build similarity maps of protein space

    Jupyter Notebook 33 11

  4. seqqc seqqc Public

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

    Groovy 28

  5. sourmashconsumr sourmashconsumr Public

    Working with the outputs of sourmash in R

    Standard ML 26 3

  6. 2023-nr-clustering 2023-nr-clustering Public

    Clustering the NCBI nr database with mmseq2 (90% length, 90% identity). Inspired by the NCBI's experimental ClusteredNR database.

    Python 23 2

Repositories

Showing 10 of 91 repositories
  • 2025-hex-assay-analysis Public
    Arcadia-Science/2025-hex-assay-analysis’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Mar 17, 2025
  • 2025-raman-spectrometer-comparison Public

    Repo for the notebook pub "Comparison of spontaneous Raman spectrometers"

    Arcadia-Science/2025-raman-spectrometer-comparison’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Mar 17, 2025
  • notebook-pub-template Public template
    Arcadia-Science/notebook-pub-template’s past year of commit activity
    CSS 4 MIT 0 3 (1 issue needs help) 0 Updated Mar 15, 2025
  • ramanalysis Public

    Package for loading and processing spectral data from Arcadia's Raman spectroscopy instruments.

    Arcadia-Science/ramanalysis’s past year of commit activity
    Python 3 MIT 0 0 0 Updated Mar 12, 2025
  • 2024-paired-token-masking Public
    Arcadia-Science/2024-paired-token-masking’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Mar 10, 2025
  • readlif Public

    Leica Image Format (LIF) file reader for Python

    Arcadia-Science/readlif’s past year of commit activity
    Python 34 GPL-3.0 13 19 3 Updated Mar 6, 2025
  • 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 5 MIT 0 13 (1 issue needs help) 0 Updated Mar 5, 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."

    Arcadia-Science/2024-publishing-v2-early-assessment’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Mar 4, 2025
  • 2024-predicting-antimicrobial-resistance Public

    Analyses of large scale E. coli metagenome diversity data

    Arcadia-Science/2024-predicting-antimicrobial-resistance’s past year of commit activity
    R 1 0 0 0 Updated Feb 28, 2025
  • arcadia-software-handbook Public

    Core software engineering guides and policies at Arcadia Science

    Arcadia-Science/arcadia-software-handbook’s past year of commit activity
    Makefile 3 CC0-1.0 0 0 0 Updated Feb 25, 2025
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