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    78 repositories

    • 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
      •55•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