An evolvable and functionally partitioned network underlies developmental remodelling in teleosts

This repository contains code, datasets, and other files used in the comparative analysis of post-embryonic development in teleost fishes. Here is the list of directories in Datasets.tar.gz and their descriptions. 00.Sequences: Contains data on genomes used in the study. 01.Kallisto: Contains the output of quantification of fastq files using Kallisto. 02.Gene_expression_and_network: Contains the RDS files for the networks and module preservation. 03.Annotation: Contains GO term enrichment result for the conserved and non-conserved modules. 04.Orthogroups: Contains output from OrthoLoger, as ortholog sets, and the ortholog sequences. 05.Phylogenomics: Contains the processed sequences for the selection analyses. These sequences consist of ortholog groups making up the conserved network and the random null set. (NOTE: this is a large repository with thousands of files). 06.CAFE5: Contains the input files, trees, and output of the CAFE analysis. 07.Systems_genes: Contains the list of genes used for module validation. 08.ZFIN: Contains the data of genetic perturbation from ZFIN. 09.Zhub: Contains UMAP plots with cell type annotation of embryonic development in zebrafish. Also contains the expression of high turnover genes from each conserved module. 10.HyPhy: Contains the output of the evolutionary analysis using HyPhy. 11.Bgee_comparative_transcriptomics: Contains the output of Bgee API calls used to obtain gene expression data of orthologs. Codes: Contains Python, Slurm, and R code used in the study. RDS: Contains various R Data Serialized objects used throughout the analyses.