Single-Cell RNA Sequencing of PMBC from Cystic Fibrosis patients

This repository contains the code used for analysis:

Single-Cell RNA Sequencing Shows that Circulating Monocytes Enriched in IFN Signaling Are Associated with Nontuberculous Mycobacteria Pulmonary Disease in Cystic Fibrosis

R scripts structure:

1: Data preparation and integration starting from STAR counts matrix.

2: Clusterization and differentially gene expression analysis

3: Signature extrapolation for selected cell population

4: Bootstrapping process for DEGs

5: Deconvolution of an external bulk dataset using EWCE

6: GSEA analysis on the external bulk dataset using EWCE

Data available:

GEO: GSE234785