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@Arcadia-Science

Arcadia Science

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 36 2

  2. seqqc seqqc Public

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

    Groovy 27

  3. ProteinCartography ProteinCartography Public

    a pipeline to build similarity maps of protein space

    Jupyter Notebook 25 10

  4. sourmashconsumr sourmashconsumr Public

    Working with the outputs of sourmash in R

    Standard ML 21 3

  5. 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 21 2

  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 15 3

Repositories

Showing 10 of 73 repositories
  • 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 6 0 Updated Aug 15, 2024
  • arcadia-pycolor Public

    tools for using the Arcadia palette in Python

    Arcadia-Science/arcadia-pycolor’s past year of commit activity
    Python 4 MIT 0 10 0 Updated Aug 14, 2024
  • test-datasets Public

    Repository for storing test datasets for workflows

    Arcadia-Science/test-datasets’s past year of commit activity
    0 1 2 1 Updated Aug 14, 2024
  • arcadia-computational-training Public

    Computational training materials developed for or delivered at Arcadia

    Arcadia-Science/arcadia-computational-training’s past year of commit activity
    Makefile 8 MIT 0 8 2 Updated Aug 13, 2024
  • 2024-peptigate-evaluation Public

    Evaluating peptide predictions made by the peptigate pipeline using orthogonal data

    Arcadia-Science/2024-peptigate-evaluation’s past year of commit activity
    Jupyter Notebook 0 MIT 0 1 0 Updated Aug 6, 2024
  • Arcadia-Science/2024-protein-universe’s past year of commit activity
    R 1 MIT 0 0 0 Updated Jul 31, 2024
  • 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 acute pain"

    Arcadia-Science/2024-sensory-neuroimaging’s past year of commit activity
    Python 0 MIT 0 0 1 Updated Jul 29, 2024
  • capsids Public

    Discovery of capsid-like proteins in diverse venomous species

    Arcadia-Science/capsids’s past year of commit activity
    Python 0 0 0 0 Updated Jul 24, 2024
  • peptigate Public

    Peptigate ("peptide" "investigate") predicts bioactive peptides from transcriptome assemblies or sets of proteins.

    Arcadia-Science/peptigate’s past year of commit activity
    Python 0 MIT 0 15 0 Updated Jul 18, 2024
  • 2024-plm-utils Public

    Minimalist tooling for working with protein language models (PLMs)

    Arcadia-Science/2024-plm-utils’s past year of commit activity
    HTML 0 MIT 0 1 0 Updated Jul 18, 2024