This repository contains the workflows for the Pipra filicauda (Wire-tailed Manakin, family: Pipridae) neurogenomics of cooperative lekking behavior.

This website houses the workflows I arrived at for the analysis of the brain and endocrine RNAseq data. The website is viewable here. It is intended as a companion to the Supplementary Materials document.

The repository branch "analysis_code" houses the Rmarkdown documents necessary to make this website, as well as the STAR mapping script. The main branch houses the data, outputs and the GO annotation process.

Please NOTE: This project uses R v4.0.2

file: data_unfiltered/Samplekey_SRA_accessions.csv is necessary to link SRA numbers for raw sequencing data to BioProject PRJNA437157, and SRR12660169-198, SRR19521260-271, SRR19521432-575 to sample codes used in the analysis.

Data Archive

The data and code necessary to recreate all the files in this repository are deposited on FigShare. Bolton, Peri; Dakin, Roslyn; Ryder, T. Brandt; Houtz, Jennifer L.; Moore, Ignacio T.; Balakrishnan, Christopher N; et al. (2023). Count Data, Phenotype Data, R Code and Results Visualizations HTML. National Museum of Natural History. Online resource. https://doi.org/10.25573/data.22186516