This workflow is designed to perform differential gene expression (DGE) analysis and other analyses on sequencing data from oviduct tissue and cell culture samples harvested from Western Viviparous (WV) and Eastern Oviparous (EO) Z. vivipara.

The folder structure contains:

01_scripts: scripts for running the analysis as well as preprocessing scripts use to produce the salmon quant data from ONT sequencing run output. All scripts were written by J. L. Smout unless otherwise credited. See script comments for full details of workflow. In brief:

	01_scripts/00_data_preprocessing/: containts scripts used to produce salmon quant files from raw read data.

	01_scripts/01_get_geneID_proteinID.sh: bash script by Hongxin Xie to extract protein IDs and corresponding gene symbols from a gff file

	01_scripts/02_get_functional_annotation.R: R script to extract functional annotation data from eggnog mapper results

	01_scripts/03_edge.R: R script to run edgeR differential gene expression analysis.

	01_scripts/04_density_and_pca.R: R script for basic data visualisation, including density plots and PCA.

	01_scripts/05_dge_analysis.R: R script for visualisation/exploration of differential gene expression results.

	01_scripts/06_pathway_analysis.R: R script for GO term analysis of DGE results.

	01_scripts/07_variance_partition.R: R script for variance partition analysis.

	01_scripts/08_wgcna.R: R script for weighted gene co-expression network analysis.

	01_scripts/09_wgcna_pathway_analysis.R: R script for GO term analysis of WGCNA results.

	01_scripts/10_summary_figures.R: R script for producing additional final figures for manuscript.

02_reference_data: Sample sheet (sample_sheet.csv) contains information on RNA samples relevant to this analysis. Genome annotation (annotation.gff & annotation.gtf), protein (protein.faa) and transcript sequences (transcript.fna and transcript.fasta) for Zootoca vivipara, downloaded from NCBI RefSeq database on 22/11/2023 at 1830 GMT, accession GCF_963506605.1. Functional annotations (eggnog.csv) were computed using eggNOG-mapper v2 (http://eggnog-mapper.embl.de/about).

This workflow is designed to perform differential gene expression (DGE) analysis and other analyses on sequencing data from oviduct tissue and cell culture samples harvested from Western Viviparous (WV) and Eastern Oviparous (EO) Z. vivipara.

The folder structure contains:

01_scripts: scripts for running the analysis as well as preprocessing scripts use to produce the salmon quant data from ONT sequencing run output. All scripts were written by J. L. Smout unless otherwise credited. See script comments for full details of workflow. In brief:

	01_scripts/00_data_preprocessing/: containts scripts used to produce salmon quant files from raw read data.

	01_scripts/01_get_geneID_proteinID.sh: bash script by Hongxin Xie to extract protein IDs and corresponding gene symbols from a gff file

	01_scripts/02_get_functional_annotation.R: R script to extract functional annotation data from eggnog mapper results

	01_scripts/03_edge.R: R script to run edgeR differential gene expression analysis.

	01_scripts/04_density_and_pca.R: R script for basic data visualisation, including density plots and PCA.

	01_scripts/05_dge_analysis.R: R script for visualisation/exploration of differential gene expression results.

	01_scripts/06_pathway_analysis.R: R script for GO term analysis of DGE results.

	01_scripts/07_variance_partition.R: R script for variance partition analysis.

	01_scripts/08_wgcna.R: R script for weighted gene co-expression network analysis.

	01_scripts/09_wgcna_pathway_analysis.R: R script for GO term analysis of WGCNA results.

	01_scripts/10_summary_figures.R: R script for producing additional final figures for manuscript.

02_reference_data: Sample sheet (sample_sheet.csv) contains information on RNA samples relevant to this analysis. Genome annotation (annotation.gff & annotation.gtf), protein (protein.faa) and transcript sequences (transcript.fna and transcript.fasta) for Zootoca vivipara, downloaded from NCBI RefSeq database on 22/11/2023 at 1830 GMT, accession GCF_963506605.1. Functional annotations (eggnog.csv) were computed using eggNOG-mapper v2 (http://eggnog-mapper.embl.de/about).