Pinned Repositories
2023-nr-clustering
Clustering the NCBI nr database with mmseq2 (90% length, 90% identity). Inspired by the NCBI's experimental ClusteredNR database.
arcadia-computational-training
Computational training materials developed for or delivered at Arcadia
metagenomics
A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies
nextflow-template-repository
GitHub template repository for creating new barebones Nextflow pipelines, using the Arcadia-Science/nextflow-template cookiecutter template
noveltree
NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.
prehgt
A pipeline for lightweight screening of Eukaryotic genomes and transcriptomes for recent HGT
ProteinCartography
a pipeline to build similarity maps of protein space
readlif
Leica Image Format (LIF) file reader for Python
seqqc
A Nextflow pipeline to identify quality control issues with new sequencing data.
sourmashconsumr
Working with the outputs of sourmash in R
Arcadia Science's Repositories
Arcadia-Science/readlif
Leica Image Format (LIF) file reader for Python
Arcadia-Science/ProteinCartography
a pipeline to build similarity maps of protein space
Arcadia-Science/noveltree
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/prehgt
A pipeline for lightweight screening of Eukaryotic genomes and transcriptomes for recent HGT
Arcadia-Science/arcadia-computational-training
Computational training materials developed for or delivered at Arcadia
Arcadia-Science/2024-Ecoli-amr-genotype-phenotype_7000strains
Arcadia-Science/arcadia-pycolor
tools for using the Arcadia palette in Python
Arcadia-Science/2024-plm-utils
Minimalist tooling for working with protein language models (PLMs)
Arcadia-Science/arcadia-software-handbook
Core software engineering guides and policies at Arcadia Science
Arcadia-Science/arcadia-phenotypeomat-protocol
phenotype-o-mat
Arcadia-Science/2024-disco-raman-hackathon
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.
Arcadia-Science/2024-protein-universe
Arcadia-Science/arcadiathemeR
Package for creating ggplot style plots in R that adhere to Arcadia Science style guidelines
Arcadia-Science/B-SOID
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.
Arcadia-Science/2023-actin-embedding
test repository for generating embedding space for actins
Arcadia-Science/2023-amblyomma-americanum-txome-assembly
Arcadia-Science/2023-koala-genomes
Arcadia-Science/2023-amblyomma-annotation
Annotation and validation of the Amblyomma americanum genome
Arcadia-Science/2023-nematode-embryo-classifier
Arcadia-Science/2023-repeats-validation
Validation of repeat expansion homologs in transcriptomes
Arcadia-Science/2024-circular-dna-workflow
This repo houses a Nextflow pipeline and Python code to scan for putative circular DNA
Arcadia-Science/2024-peptigate-evaluation
Evaluating peptide predictions made by the peptigate pipeline using orthogonal data
Arcadia-Science/2024-phenotypeomat
Arcadia-Science/2024-sensory-neuroimaging
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/arcadia-twitter-collections
Services to manage set of Twitter collections for Arcadia's publications
Arcadia-Science/capsids
Discovery of capsid-like proteins in diverse venomous species
Arcadia-Science/Fungal-Secondary-Actin-Pilot
This pilot investigates the distribution of divergent fungal actins and their potential correlation with specific fungal traits
Arcadia-Science/peptigate
Peptigate ("peptide" + "investigate") predicts bioactive peptides from transcriptome assemblies or sets of proteins.
Arcadia-Science/protein-data-curation
Arcadia-Science/test-datasets
Repository for storing test datasets for workflows