README.md

trained_immunity

R scripts of trained immunity scRNA-seq projects

load and cluster the in vitro data

loading_and_clustering.R

get expressed genes from a seurat object (default in > 10% of the cells)

get_expressed_genes.R

Codes to generate the merged violin plots

ViolinPlots.R

heatmap and clustering based on trained immunity signatures

TrainedSubsets.R

calculate the cellproprotion of trained cells

cellproportion.R

analyses for the in vivo data

invivo_data.R

data accessibility:

Raw scRNA-seq data has been deposited at the European Genome-phenome Archive (EGA), under accession number E-MTAB-9702;
Seurat object with count matrix and metadata has been deposited in Cloud service of Helmholtz Center: https://nubes.helmholtz-berlin.de/s/nwkJ3XECGMcx4yo,
with an extract key as "TrainedImmunityHZI"

For more information, please contact zhangbowen3187@gmail.com