Repositories list

• 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

• 2024-paired-token-masking

  Public
  Makefile

  •

  MIT License

  •0•0•0•1•Updated Nov 1, 2024Nov 1, 2024

• arcadia-pycolor

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

  Python

  •

  MIT License

  •0•4•12•0•Updated Oct 29, 2024Oct 29, 2024

• 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 Oct 10, 2024Oct 10, 2024

• arcadia-phenotypeomat-protocol

  Public
  phenotype-o-mat

  Python

  •

  MIT License

  •0•2•2•0•Updated Sep 24, 2024Sep 24, 2024

• readlif

  Public
  Leica Image Format (LIF) file reader for Python

  Python

  •

  GNU General Public License v3.0

  •13•32•16•2•Updated Sep 18, 2024Sep 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.

  Nextflow

  •

  GNU Affero General Public License v3.0

  •3•17•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•5•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

• ProteinCartography

  Public
  a pipeline to build similarity maps of protein space

  Jupyter Notebook

  •

  MIT License

  •10•30•7•0•Updated Jul 15, 2024Jul 15, 2024

• prehgt

  Public
  A pipeline for lightweight screening of Eukaryotic genomes and transcriptomes for recent HGT

  Jupyter Notebook

  •

  MIT License

  •6•12•14•1•Updated Jun 18, 2024Jun 18, 2024

• 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 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

• B-SOID

  Public
  CLI adaptation of B-SOiD. Behavioral segmentation of open field in DeepLabCut, or B-SOID ("B-side"), is a pipeline that pairs unsupervised pattern recognition with supervised classification to achieve fast predictions of behaviors that are not predefined by users.

  Python

  •

  GNU General Public License v3.0

  •57•1•0•0•Updated May 15, 2024May 15, 2024

• 2024-phenotypeomat

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Apr 23, 2024Apr 23, 2024

• Fungal-Secondary-Actin-Pilot

  Public
  This pilot investigates the distribution of divergent fungal actins and their potential correlation with specific fungal traits

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Mar 4, 2024Mar 4, 2024

• 2023-actin-embedding

  Public
  test repository for generating embedding space for actins

  Jupyter Notebook

  •0•0•1•0•Updated Feb 28, 2024Feb 28, 2024

• 2023-amblyomma-annotation

  Public
  Annotation and validation of the Amblyomma americanum genome

  R

  •

  MIT License

  •0•0•0•0•Updated Feb 22, 2024Feb 22, 2024

• protein-data-curation

  Public
  Python

  •

  GNU Affero General Public License v3.0

  •0•0•1•0•Updated Feb 1, 2024Feb 1, 2024

• 2023-amblyomma-americanum-txome-assembly

  Public
  Python

  •

  MIT License

  •0•0•2•0•Updated Jan 31, 2024Jan 31, 2024

• 2023-nematode-embryo-classifier

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 30, 2024Jan 30, 2024