The default collection of frequently used gene-sets

This data.frame contains all gene-sets SPATA offers by default. If no other gene-set-data.frame path has been specified in the argument gene_set_path of the function initiateSpataObject_10X() it will use this data.frame as the default for slot @used_genesets.

data(gsdf)

Format

A data.frame with 936.495 rows and two variables.

ont

Character. The gene set names that have to be separated by an underscore '_', which separates the gene-set's class belonging from the actual gene-set name.

gene

Character. The genes that belong to the respective gene-set denoted as character values.

Source

https://www.gsea-msigdb.org/gsea/index.jsp

Details

Number of different gene-sets: 11654

Gene set classes:

• BP.GO: Biological processes - gene ontology

• CC.GO: Cellular componenents - gene-ontology

• MF.GO: Molecular functions - gene-ontology

• HM: Hallmark gene sets

• BC: Biocarta gene sets

• RCTM: Reactome gene sets