https://github.com/weinstockj/rnaseq-perturbation-cd4-pipeline

https://github.com/weinstockj/rnaseq-perturbation-cd4-pipeline

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• Host: GitHub
• URL: https://github.com/weinstockj/rnaseq-perturbation-cd4-pipeline
• Owner: weinstockj
• Created: 2023-02-01T17:56:48.000Z (almost 2 years ago)
• Default Branch: master
• Last Pushed: 2024-07-24T16:26:54.000Z (5 months ago)
• Last Synced: 2024-07-24T19:01:07.485Z (5 months ago)
• Language: R
• Size: 163 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
This repo contains the bioninformatics processing steps (primarily alignment, QC, gene quantification) and most downstream analyses 

included in [Gene regulatory network inference from CRISPR perturbations in primary CD4+ T cells elucidates the genomic basis

of immune disease](https://www.biorxiv.org/content/10.1101/2023.09.17.557749v2). 

## Requirements

The data processing pipeline uses Snakemake. You can recreate the mamba/conda environment here using

`mamba env create --file environment.yaml` . Please note that the Snakefile does contain a few 

hardcoded paths, which are written before the first rule. 

This repo also contains R code to perform several analyses. You can recreate the R envinroment

using [renv](https://rstudio.github.io/renv/index.html), i.e., 

`install.packages("renv"); renv::restore()` . The R analyses are implemented using a single large

[targets](https://books.ropensci.org/targets/) workflow file. 

## Contact

For questions about the code, please file an issue here or contact Josh Weinstock .