README.rmd

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# Astrocytes_editing

## Background

This repository contains analysis code for the publication found [here](), which explored the response of astrocytes, neurons and astro-neuronal co-cultures to alpha-synuclein oligomers. The analysis includes work shared between two repositories:

- The repository at [https://github.com/karishdsa/ipscAstrNeurCocul](https://github.com/karishdsa/ipscAstrNeurCocul) contains single cell and bulk RNA sequencing analysis of the cell culture models utilised in the study.
- This current repository contains the analysis of RNA editing in the cell culture models, as well as in a [published dataset](https://link.springer.com/article/10.1007/s00401-021-02343-x) of post-mortem brain samples.


## Code contents

Within this repository you will find:

| Directory | Description |
| --------- | --------------------------------------------------------------------------- |
| [docs](docs) | Contains all `.Rmd`s and their corresponding `.html`s describing analyses performed for this project. These can be view interactively at: [link](#TODO)|
| [logs](logs) | For any scripts that were run outside of an `.Rmd` (e.g. scripts from the [scripts](scripts) directory), a log file was recorded and can be accessed here. |
| [scripts](scripts)| Contains non R related scripts. |
| [raw_data](raw_data) | External tables used in analyses. |
| [renv](renv) | `renv`-related scripts |
| [results](results) | Results from all analyses. |
| [rscripts](rscripts) | Contains analysis scripts. Each script contains a one-line description and is also referenced in its corresponding `.Rmd`. |

## Reproducibility
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### `renv`
<!-- Consider using renv for reproducibility. Delete this section if you will not be doing this. -->

*TODO: consider setting up `renv`, using the following [guide](https://rstudio.github.io/renv/articles/renv.html. Modify text below as appropriate.* 

This repository uses [`renv`](https://rstudio.github.io/renv/index.html) to create a reproducible environment for this R project. 

1. When you first launches this project, `renv` should automatically bootstrap itself, thereby downloading and installing the appropriate version of `renv` into the project library. 
2. After this has completed, you can use `renv::restore()` to restore the project library locally on your machine.

For more information on collaborating with `renv`, please refer to this [link](https://rstudio.github.io/renv/articles/collaborating.html).

### `DESCRIPTION`
<!-- Consider using renv for reproducibility. Delete this section if you will not be doing this. -->



## License

The code in this repository is released under an MIT license. This repository is distributed in the hope that it will be useful to the wider community, but without any warranty of any kind. Please see the [LICENSE](LICENSE) file for more details. 

## Citation

The RNA editing analysis was undertaken with [JACUSA2](https://github.com/dieterich-lab/JACUSA2). Converting the output to bed format was undertaken using a custom script written by [George Young](https://www.linkedin.com/in/george-young-6153a11bb/?originalSubdomain=uk).