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 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 of post-mortem brain samples. The results of this repository can be viewed interactively at
Within this repository you will find:
| Directory | Description |
|---|---|
| docs | Contains all .Rmds and their corresponding .htmls describing analyses performed for this project. These can be view interactively at: https://aaronwagen.github.io/Astrocytes_editing/ |
| scripts | Contains all non R and R related scripts. |
| renv | renv-related scripts |
| functions | Contains r functions used throughout the analysis, and common arguments and filters .Rmd. |
This repository uses renv
to create a reproducible environment for this R project.
- When you first launches this project,
renvshould automatically bootstrap itself, thereby downloading and installing the appropriate version ofrenvinto the project library. - 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.
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 file for more details.
The RNA editing analysis was undertaken with JACUSA2. Converting the output to bed format was undertaken using a custom script written by George Young.