The repository provides the computational framework and results for:

Functional analysis of miR-2954: Investigating the effects of miR-2954 knockout in chicken models.

Evolutionary genomics analyses: Exploring the evolutionary pressures and adaptations related to dosage-sensitive genes on the Z chromosome.

Bioinformatics workflows: Scripts for RNA sequencing data processing, target prediction, and expression analysis.

Repository Structure and Contents

The repository is organized into several directories and R Markdown files, each corresponding to a specific analysis or set of data:

Current-Z to Prot-Z analysis: Contains scripts and data for analyzing gene expression changes between current Z-linked genes and their ancestral proto-Z counterparts.

Identify Conserved Target Sites: Scripts to identify conserved target sites for miR-2954 across different avian species, potentially focusing on chicken and zebra finch.

Identify Developmentally Expressed Genes: Analysis to pinpoint genes that exhibit significant expression changes during different developmental stages.

Long RNA-seq Alignment & Read Count: Workflow and scripts for aligning long RNA sequencing reads and quantifying gene expression levels.

Short RNA Sequencing Alignment & Read Count: Workflow and scripts for aligning short RNA sequencing reads (likely for microRNA analysis) and quantifying their expression.

Survival_Plots: Scripts for generating survival plots, likely related to the viability assessment of miR-2954 knockout models.

TargetScan context+ score calculation: Code to calculate TargetScan context+ scores, which predict the efficacy of microRNA binding to target sites.

Translatome Current-Z to Prot-Z analysis.Rmd: R Markdown file for analyzing translatome data, comparing current Z-linked genes to proto-Z genes, focusing on translational efficiency.

Translatome F-M-TE-ratio.Rmd: R Markdown file for analyzing translatome data, specifically looking at translational efficiency ratios between female and male samples.

Translatome F-M-ratio.Rmd: R Markdown file for analyzing translatome data, focusing on overall expression ratios between female and male samples.

Translatome Mko-Mwt-ratio.Rmd: R Markdown file for analyzing translatome data, comparing male knockout (Mko) to male wild-type (Mwt) samples.

miR-2954 Target Prediction: Scripts and data for predicting the target genes of miR-2954.