Arcadia Science

ProteinCartography

a pipeline to build similarity maps of protein space

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

arcadia-computational-training

Computational training materials developed for or delivered at Arcadia

arcadia-pycolor

tools for using the Arcadia palette in Python

arcadia-software-handbook

Core software engineering guides and policies at Arcadia Science

arcadia-phenotypeomat-protocol

phenotype-o-mat

arcadiathemeR

Package for creating ggplot style plots in R that adhere to Arcadia Science style guidelines

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.

chlamy-comparison

This repository contains code for image processing and analysis to compare phenotypes of interfertile algal species.

2023-actin-embedding

test repository for generating embedding space for actins

2023-amblyomma-americanum-txome-assembly

2023-focus-filtering

This is a repository for code and analysis related to feature- and edge-detection algorithms for identifying frames of cells in focus.

2023-koala-genomes

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.

microchamber-analysis

2023-amblyomma-annotation

Annotation and validation of the Amblyomma americanum genome

2023-nematode-embryo-classifier

2023-repeats-profiling

Profiling repeat expansions across the tree of life with a specific focus on disease-causing REs

2023-repeats-validation

Validation of repeat expansion homologs in transcriptomes

2024-phenotypeomat

2024-plm-utils

Minimalist tooling for working with protein language models (PLMs)

2024-protein-universe

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-twitter-collections

Services to manage set of Twitter collections for Arcadia's publications

capsids

Discovery of capsid-like proteins in diverse venomous species

Fungal-Secondary-Actin-Pilot

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

peptigate

Peptigate ("peptide" + "investigate") predicts bioactive peptides from transcriptome assemblies or sets of proteins.

protein-data-curation

test-datasets

Repository for storing test datasets for workflows