# Overview
This repository contains the code used to perform genomics and transcriptomics analysis from the pre-print manuscript:

"Oliveira, Daniel Siqueira et al. Transposable elements as evolutionary driving force to host shift in cactophilic Drosophila species. bioRxiv, 10/24/2024, doi: 10.1101/2024.03.27.587021"

### Instructions and file descriptions:

- [Differential expresssion analysis](https://github.com/OliveiraDS-hub/Pipelines-Cactophilic-Drosophila-Species/tree/main/Differential-expression)
- [Gene annotation](https://github.com/OliveiraDS-hub/Pipelines-Cactophilic-Drosophila-Species/tree/main/Gene-annotation)
- [Permutation tests](https://github.com/OliveiraDS-hub/Pipelines-Cactophilic-Drosophila-Species/tree/main/Permutation-test)
- [Positive selection test](https://github.com/OliveiraDS-hub/Pipelines-Cactophilic-Drosophila-Species/tree/main/Positive_selection_test)
- [TE annotation](https://github.com/OliveiraDS-hub/Pipelines-Cactophilic-Drosophila-Species/tree/main/TEannotation)
- [Transcription factor binding sites analysis](https://github.com/OliveiraDS-hub/Pipelines-Cactophilic-Drosophila-Species/tree/main/TFBSs_analysis)
