The Hitchhiker's Guide to scRNA-seq course

This repository comprises the intermediate results, data, and the respective script to create it, to be use on the second day of the course The Hitchhiker's Guide to scRNA-seq (08-12/07/2024, iMM, Lisbon, Portugal), focused on integration. 

File description: 

data: 

pbmcref.rds: a Seurat R object of a reference of PBMCs retrieved from the R package SeuratData (v.0.2.2.9001)

pbmc3k_panc8.rds: a Seurat R object of two data sets - 3k human PBMCs from 10X Genomics and pancreatic islets from indrop1 - retrieved from SeuratData package (v.0.2.2.9001) 

jurkat.rds: a Seurat R object comprising three data sets - Jurkat, HEK293T and Jurkat:HEK293T (50:50) - retrieved from 10X genomics and published by Zheng et al., 2017

ifnb.rds: a Seurat R object of two human PBMCs data sets - resting/control and interferon-stimulated - retrieved from the R package SeuratData (v.0.2.2.9001)

covid.rds: a Seurat R object of a COVID-19 PBMCs data set from Guo et al., 2020 retrieved from cziscience

01_create_datasets.R: R script used to retrieve and parse all the Seurat R objects mentioned above

results.zip: compressed folder with intermediate results used for the hands-on exercises