README.Rmd

---
title: "README"
author:
output: github_document
date: "`r Sys.Date()`"
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# The Landscape of *SETBP1* tissue-specific gene expression and regulation across human tissues

## Authors
**Jordan H. Whitlock Elizabeth J. Wilk, Timothy C. Howton, Amanda D. Clark, Brittany N. Lasseigne**

The University of Alabama at Birmingham (UAB), Heersink School of Medicine, Department of Cell, Developmental and Integrative Biology (CDIB)

[The Lasseigne Lab](https://www.lasseigne.org/)

<img src="https://www.lasseigne.org/img/main/lablogo.png" width="90" height="90">

## Purpose 

**The purpose of this research is to investigate the tissue-specific expression and regulatory landscape of human *SETBP1* in GTEx tissues**
This repository contains the code and accompanying data for our analysis of the tissue-specific expression and regulation of transcription factor (TF) *SETBP1* across 31 non-diseased human tissues part of the Genotype-tissue expression project (GTEx). This project is hypothesis generating, therefore emphasizing the role of different contexts, such as tissues, and the role they may play in disease when a variant is introduced.

## Scripts

Here we provide a framework to investigate the following: 

- [Tissue-specific expresion of *SETBP1* and its known targets](https://github.com/lasseignelab/230323_JW_DiseaseNetworks/tree/main/src/Tissue_Expression)
```{r echo = FALSE}
fs::dir_tree("src/Tissue_Expression")
```

- [Construction of tissue-specific gene regulatory networks](https://github.com/lasseignelab/230323_JW_DiseaseNetworks/tree/main/src/GTEx_PANDA)
```{r echo = FALSE}
fs::dir_tree("src/GTEx_PANDA")
```
  - Information on Network inputs and how to produce them can be found [here](https://github.com/lasseignelab/230323_JW_DiseaseNetworks/tree/main/src/panda_input_construction).
```{r echo = FALSE}
fs::dir_tree("src/panda_input_construction")
```

- [Tissue-specific community detection](https://github.com/lasseignelab/230323_JW_DiseaseNetworks/tree/main/src/community_detection)
```{r echo = FALSE}
fs::dir_tree("src/community_detection")
```

- [SETBP1 TF activity analysis](https://github.com/lasseignelab/230323_JW_DiseaseNetworks/tree/main/src/tf_activity)
```{r echo = FALSE}
fs::dir_tree("src/tf_activity")
```

- [TF targeting](https://github.com/lasseignelab/230323_JW_DiseaseNetworks/tree/main/src/tf_targeting)
```{r echo = FALSE}
fs::dir_tree("src/tf_targeting")
```

- [Tissue-specific edge identification](https://github.com/lasseignelab/230323_JW_DiseaseNetworks/tree/main/src/tissue_specific_edges)
```{r echo = FALSE}
fs::dir_tree("src/tissue_specific_edges")
```

*However, this code can be adapted and applied to other genes or TFs.*

## Dependencies and Resources
This analysis was carried out in Docker using R version 4.1.3. TF activity inference using [decoupleR](), [PANDA]() tissue-specific regulatory network generation, and tissue-specific edge identification were run using the Docker on UAB's high performance computing Cluster. Bash scripts including resources used are included in this repository. The containers have been made publicly available on Zenodo:

[put Zenodo buttons here]

## Funding 

List project funding sources. 

## Acknowledgements 

List project acknowledgements.

## License 

[![License](https://img.shields.io/badge/LICENSE-MIT_License-yellow)](https://github.com/lasseignelab/230323_JW_DiseaseNetworks/blob/main/LICENSE)

This repository is licensed under the MIT License, see LICENSE documentation within this repository for more details.