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    85 repositories

    • notebook-pub-template

      Public template
      Jupyter Notebook
      •
      MIT License
      •0•1•1•1•Updated Jan 31, 2025Jan 31, 2025

    • 2024-paired-token-masking

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

    • arcadia-software-handbook

      Public
      Core software engineering guides and policies at Arcadia Science
      Makefile
      •
      Creative Commons Zero v1.0 Universal
      •0•3•0•0•Updated Jan 29, 2025Jan 29, 2025

    • .github

      Public
      0•0•0•0•Updated Jan 29, 2025Jan 29, 2025

    • arcadia-twitter-collections

      Public
      Services to manage set of Twitter collections for Arcadia's publications
      Python
      •
      Creative Commons Zero v1.0 Universal
      •0•1•0•0•Updated Jan 24, 2025Jan 24, 2025

    • readlif

      Public
      Leica Image Format (LIF) file reader for Python
      Python
      •
      GNU General Public License v3.0
      •13•33•18•4•Updated Jan 13, 2025Jan 13, 2025

    • 2024-organismal-selection

      Public
      Code associated with the pub "Leveraging evolution to identify novel organismal models of human biology"
      R
      •
      MIT License
      •0•0•0•0•Updated Jan 8, 2025Jan 8, 2025

    • 2024-worm-tracking

      Public
      Tracking C. elegans motility in brightfield movies
      Jupyter Notebook
      •
      MIT License
      •0•0•2•0•Updated Jan 7, 2025Jan 7, 2025

    • 2023-amblyomma-americanum-diffex

      Public
      Exploring A. americanum differential expression and expression across tissues
      Jupyter Notebook
      •
      MIT License
      •0•0•3•0•Updated Dec 23, 2024Dec 23, 2024

    • arcadia-pycolor

      Public
      Python package for styling plots according to Arcadia's style guide
      Python
      •
      MIT License
      •0•4•12•0•Updated Dec 20, 2024Dec 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."
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 19, 2024Dec 19, 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."
      Jupyter Notebook
      •
      MIT License
      •0•0•2•0•Updated Dec 14, 2024Dec 14, 2024

    • ProteinCartography

      Public
      a pipeline to build similarity maps of protein space
      Jupyter Notebook
      •
      MIT License
      •10•30•7•0•Updated Dec 10, 2024Dec 10, 2024

    • 2024-chelicerate-phylogenomics

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Nov 25, 2024Nov 25, 2024

    • arcadiathemeR

      Public
      Package for creating ggplot style plots in R that adhere to Arcadia Science style guidelines
      R
      •
      Other
      •0•1•6•0•Updated Nov 6, 2024Nov 6, 2024

    • 2024-unicellular-tracking

      Public
      Image analysis workflows for tracking unicellular organisms
      Jupyter Notebook
      •
      MIT License
      •0•0•3•0•Updated Nov 6, 2024Nov 6, 2024

    • arcadia-phenotypeomat-protocol

      Public
      phenotype-o-mat
      Python
      •
      MIT License
      •0•2•2•0•Updated Sep 24, 2024Sep 24, 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.
      Nextflow
      •
      GNU Affero General Public License v3.0
      •4•20•19•1•Updated Sep 9, 2024Sep 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"
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 9, 2024Sep 9, 2024

    • 2024-circular-dna-workflow

      Public
      This repo houses a Nextflow pipeline and Python code to scan for putative circular DNA
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 22, 2024Aug 22, 2024

    • 2024-Ecoli-amr-genotype-phenotype_7000strains

      Public
      Jupyter Notebook
      •
      MIT License
      •0•4•0•0•Updated Aug 21, 2024Aug 21, 2024

    • test-datasets

      Public
      Repository for storing test datasets for workflows
      1•0•2•0•Updated Aug 19, 2024Aug 19, 2024

    • arcadia-computational-training

      Public
      Computational training materials developed for or delivered at Arcadia
      Makefile
      •
      MIT License
      •0•9•8•2•Updated Aug 13, 2024Aug 13, 2024

    • 2024-peptigate-evaluation

      Public
      Evaluating peptide predictions made by the peptigate pipeline using orthogonal data
      Jupyter Notebook
      •
      MIT License
      •0•0•1•0•Updated Aug 6, 2024Aug 6, 2024

    • 2024-protein-universe

      Public
      R
      •
      MIT License
      •0•1•0•0•Updated Jul 31, 2024Jul 31, 2024

    • capsids

      Public
      Discovery of capsid-like proteins in diverse venomous species
      Python
      •0•0•0•0•Updated Jul 24, 2024Jul 24, 2024

    • peptigate

      Public
      Peptigate ("peptide" + "investigate") predicts bioactive peptides from transcriptome assemblies or sets of proteins.
      Python
      •
      MIT License
      •1•1•15•0•Updated Jul 18, 2024Jul 18, 2024

    • 2024-plm-utils

      Public
      Minimalist tooling for working with protein language models (PLMs)
      HTML
      •
      MIT License
      •1•3•1•0•Updated Jul 18, 2024Jul 18, 2024

    • prehgt

      Public
      A pipeline for lightweight screening of Eukaryotic genomes and transcriptomes for recent HGT
      Jupyter Notebook
      •
      MIT License
      •6•13•14•1•Updated Jun 18, 2024Jun 18, 2024

    • 2024-disco-raman-hackathon

      Public
      This repo is intended to hold code and results pertaining to the raman hackathon carried out by the discovery team at the discovery offsite in March 2024.
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated May 31, 2024May 31, 2024