README

This folder contains the scripts to analyse the single-cell RNAseq data from the infected placental explants.

The order to run this analysis is:

1. data_integration: scripts to read, integrate and annotate the data.
2. diffGeneExpression: scripts to run differential expression analysis.
3. cellPhoneDB: scripts to run cellphoneDB v4.
4. plots_forFigures: scripts to generate most of the plots included in the article's Figures.
5. PBMC_10k: scripts to analyse the 10k PBMCs dataset from 10x Genomics.
6. luminex: analysis of luminex data (protein levels) from supernatant cytokines.