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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 2

  2. readlif readlif Public

    Leica Image Format (LIF) file reader for Python

    Python 31 13

  3. ProteinCartography ProteinCartography Public

    a pipeline to build similarity maps of protein space

    Jupyter Notebook 30 9

  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 77 repositories
  • 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 Oct 29, 2024
  • 2024-paired-token-masking Public
    Arcadia-Science/2024-paired-token-masking’s past year of commit activity
    Makefile 0 MIT 0 0 1 Updated Oct 24, 2024
  • 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 Oct 10, 2024
  • arcadia-phenotypeomat-protocol Public

    phenotype-o-mat

    Arcadia-Science/arcadia-phenotypeomat-protocol’s past year of commit activity
    Python 2 MIT 0 2 0 Updated Sep 24, 2024
  • readlif Public

    Leica Image Format (LIF) file reader for Python

    Arcadia-Science/readlif’s past year of commit activity
    Python 31 GPL-3.0 13 16 2 Updated Sep 18, 2024
  • 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.

    Arcadia-Science/noveltree’s past year of commit activity
    Nextflow 16 AGPL-3.0 3 19 1 Updated Sep 9, 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 0 Updated Sep 9, 2024
  • 2024-circular-dna-workflow Public

    This repo houses a Nextflow pipeline and Python code to scan for putative circular DNA

    Arcadia-Science/2024-circular-dna-workflow’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Aug 22, 2024
  • 2024-Ecoli-amr-genotype-phenotype_7000strains Public
    Arcadia-Science/2024-Ecoli-amr-genotype-phenotype_7000strains’s past year of commit activity
    Jupyter Notebook 5 MIT 0 0 0 Updated Aug 21, 2024
  • test-datasets Public

    Repository for storing test datasets for workflows

    Arcadia-Science/test-datasets’s past year of commit activity
    0 1 2 0 Updated Aug 19, 2024
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