Atlas-level data integration of BAL samples from severe COVID-19

This repository contains code for the processing and analysis of scRNA-seq samples from patients with severe COVID-19.

Directory Structure

bin/ - Scripts used for the analysis
docs/ - Document files
data/ - Data output (large, not included in git)
workflows/ - Workflows executing scripts in bin/
reports/ - Reports for exploratory analysis
analysis/ - Analysis output (not included in git)
man/ - Manuals explaining the rationale behind analyses
envs/ - conda environment YAML files
LICENSE - The project license

Data Availability

Shared on web portal: TODO

Download as part of workflows, described in bin/dataset_*

Analysis workflows

The analysis workflow include download & setup of datasets. Quality control, data integration, cell annotation, evaluation using (scIB) metrics and visualization of reports.

The workflows are written in bash and can be submitted using SLURM.

To reproduce the analysis please

Install conda (follow instructions and accept defaults), close and re-open the console

curl -o miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash miniconda.sh
rm miniconda.sh

Install mamba

conda install -c bioconda mamba -y
mamba init

Clone and enter the git repository (if you want to specify the directory replace '~' with your local path)

cd ~
git clone https://github.com/saliba-lab/covid19-bal-atlas-integration.git
cd covid19-bal-atlas-integration

Create conda environments

mamba env create -f envs/R.yml
conda env create -f envs/integration.yml
conda env create -f envs/scib.yml

Execute workflows (beginning with the count matrix)
```
bash workflows/setup_BCB.sh
```

Addendum

To use nextflow workflows please install java

sudo apt install default-jre