Evolutionary repeatability

This repo contains python code and intermediate data used in the paper: Repeatability of gene expression evolution in experimental environmental adaptation?

Clone this repository

git clone https://github.com/jiachenli12/evo_repeatability.git

Directories in this repo:

fig_reproduction:

This directory contains code and relevant data to reproduce main and supplementary figures presented in the paper.

src:

This directory contains custom code to examine the three definitions of gene expression evoution repeatability.

1. deg_def1: the first definition of evolutionary repeatability. The script generates the null distribution of DEGs that are shared between parallel line pairs and >2 parallel lines. Observed number of shared DEGs and Z-scores are directly annotated on the plot.

2. same_direction_def2: the second definition of evolutionary repeatability

3. magnitude_def3: the third definition of evolutionary repeatability

4. dice_coefficient: compute dice's coefficent

Dependency: Python3