Atlas feature selection benchmarking

This repository contains code for benchmarking the effect of feature selection on scRNA-seq atlas construction and use.

For more information please refer to the documentation on the wiki.

Directory structure

analysis/ - Notebooks used to perform analysis of the results
- R/ - R functions used in the analysis notebooks
bin/ - Scripts used in Nextflow workflows
- functions/ - Functions used across multiple scripts
conf/ - Nextflow configuration files
data/ - Data files used in the analysis. Metric score files can downloaded from figshare.
- selected-features/ - Selected features files for each dataset. Can be downloaded from figshare.
envs/ - conda environment YAML files
output/ - Output from Nextflow workflows (not included in git)
reports/ - RMarkdown files and functions for output reports generated by the pipeline
work/ - The Nextflow working directory (not included in git)
workflows/ - Nextflow workflow files
LICENSE - The project license
main.nf - Main Nextflow workflow file
nextflow.config - Main Nextflow config file
README.md - This README
style_bin.sh - A script for styling the files in bin/

Data files for this project are available from figshare. The analysis reports in the analysis/ directory assume:

Metric files are downloaded to the data/ directory
Selected features files are downloaded to the data/selected-features/ directory