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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 32 13

  3. ProteinCartography ProteinCartography Public

    a pipeline to build similarity maps of protein space

    Jupyter Notebook 30 10

  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 25 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 84 repositories
  • notebook-pub-template Public
    Arcadia-Science/notebook-pub-template’s past year of commit activity
    Jupyter Notebook 1 MIT 0 0 0 Updated Dec 24, 2024
  • readlif Public

    Leica Image Format (LIF) file reader for Python

    Arcadia-Science/readlif’s past year of commit activity
    Python 32 GPL-3.0 13 18 3 Updated Dec 24, 2024
  • 2023-amblyomma-americanum-diffex Public

    Exploring A. americanum differential expression and expression across tissues

    Arcadia-Science/2023-amblyomma-americanum-diffex’s past year of commit activity
    Jupyter Notebook 0 MIT 0 3 0 Updated Dec 23, 2024
  • 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 4 MIT 0 12 (1 issue needs help) 0 Updated Dec 20, 2024
  • 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 Dec 19, 2024
  • 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 Dec 19, 2024
  • 2024-organismal-selection Public
    Arcadia-Science/2024-organismal-selection’s past year of commit activity
    R 0 MIT 0 0 0 Updated Dec 14, 2024
  • 2024-chlamy-mutant-motility-pub Public

    Collection of data, code, scripts, and notebooks accompanying the pub "Rescuing Chlamydomonas Motility in Mutants Modeling Spermatogenic Failure."

    Arcadia-Science/2024-chlamy-mutant-motility-pub’s past year of commit activity
    Jupyter Notebook 0 MIT 0 2 0 Updated Dec 14, 2024
  • ProteinCartography Public

    a pipeline to build similarity maps of protein space

    Arcadia-Science/ProteinCartography’s past year of commit activity
    Jupyter Notebook 30 MIT 10 7 0 Updated Dec 10, 2024
  • 2024-chelicerate-phylogenomics Public
    Arcadia-Science/2024-chelicerate-phylogenomics’s past year of commit activity
    HTML 0 MIT 0 0 0 Updated Nov 25, 2024
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