Repositories list

• arcadia-pycolor

  Public
  Python package for styling plots according to Arcadia's style guide

  Python

  •

  MIT License

  •0•4•13•0•Updated Feb 14, 2025Feb 14, 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 Feb 14, 2025Feb 14, 2025

• ramanalysis

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

  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 13, 2025Feb 13, 2025

• readlif

  Public
  Leica Image Format (LIF) file reader for Python

  Python

  •

  GNU General Public License v3.0

  •13•33•19•3•Updated Feb 6, 2025Feb 6, 2025

• 2024-ProteinCartography-dCK-validation

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 5, 2025Feb 5, 2025

• 2024-paired-token-masking

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Feb 3, 2025Feb 3, 2025

• notebook-pub-template

  Public template
  Jupyter Notebook

  •

  MIT License

  •0•1•1•1•Updated Feb 3, 2025Feb 3, 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

• 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

• 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•31•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•7•0•Updated Nov 6, 2024Nov 6, 2024

• 2024-unicellular-tracking

  Public
  Image analysis workflows for tracking unicellular organisms

  Jupyter Notebook

  •

  MIT License

  •0•1•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