This repository contains analysis code for the publication found here, which applied paired bulk-tissue and single-nucleus RNA-sequencing to anterior cingulate cortex samples derived from 28 individuals, including healthy controls and Lewy body disease cases.
Analyses were shared between two groups, thus code herein relates to:
- Processing and analysis bulk-tissue RNA-sequencing data
- Generation of sLDSC outputs
- Generation of manuscript figures
Code used to process and analyse single-nucleus RNA-sequencing data and to generate H-MAGMA outputs is available at: https://github.com/rahfel/snRNAseqProcessingSteps.
If you use any of the code or data from this repository, please cite our paper.
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.
All .Rmds can be viewed as interactive .htmls here: https://rhreynolds.github.io/LBD-seq-bulk-analyses/.
Within this repository you will otherwise find:
| Directory | Description |
|---|---|
| docs | Contains all .Rmds and their corresponding .htmls describing analyses performed for this project. These can be view interactively at: https://rhreynolds.github.io/LBD-seq-bulk-analyses/ |
| man | Contains a figure used in overview.Rmd |
| misc_scripts | Contains analysis scripts that were run separate from .Rmds. Each script contains a one-line description and is also referenced in its corresponding .Rmd. |
| nohup_logs | For any scripts that were run outside of an .Rmd (e.g. scripts from the misc_scripts directory), a log file was recorded and can be accessed here. |
| R | Various functions called in docs and misc_scripts. |