Monocytes_leishmania

Repository under progress

Update 16/06/23: Repository will be updated shortly after publication to include the download of the count matrix from GEO.

Update 03/07/23: Link to download the count matrix has been updated.

This repository contains scripts for the scRNAseq analysis of monocytes infected by Leishmania

Data Accessibility

For now, the count matrix can be downloaded from the Helmholtz Cloud. The count matrix should be manually download and place in the data folder of the repository.

Repository Structure

data: Directory containing required raw data. The count matrix should be manually placed in this directory too. A metadata table describing relevant experimental information for each single-cell library is also included (Info_experiment.csv)

analysis: Directory containing the R scripts.

outputs: This directory is created when running the scripts. It will contain the processed data and different results including differentially expressed gene tables, annotated Seurat objects, plots...

Code Execution

1- Download repository

Option 1: Download manually the repository as a ZIP archive and extract it locally on your computer

Option 2: Clone the repository

git clone https://github.com/saliba-lab/Monocytes_leishmania.git
cd Monocytes_leishmania/analysis

2- Install R and python dependencies

See Dependencies section.

3- Run sequentially the scripts in the analysis directory

Make sure to set the analysis directory as the working directory when running the scripts.

Dependencies

Required R libraries

• R 4.0.3
• dplyr 1.0.10
• stringr 1.4.0
• biomaRt 2.46.3
• tibble 3.1.8
• ggplot2 3.4.0
• cowplot 1.1.1
• scales 1.2.1
• gridExtra 2.3
• SCnorm 1.12.1
• SingleCellExperiment 1.12.0
• Seurat 4.0.0
• harmony 0.1.1
• igraph 1.2.6
• leidenbase 0.1.3
• tidyr 1.2.1
• RColorBrewer 1.1-3