baderPathways: Pathway annotations from Bader Lab

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Pathway annotations from Bader Lab

Description

Updated list of gene sets used for enrichment analysis. Consolidated by Bader Lab, includes KEGG, Msigdb, NCI, IOB, NetPath, HumanCyc, Reactome, GO, Panther. http://baderlab.org/GeneSets

Usage

{
data(baderPathways)


# To update list:

# specify location of input data
# directory <- "D:/Users/Nick/Dropbox/PDF Projects - JM/Data/CRISPR screen/GIN Data/"
# file.pathways <- list(
#   Hs.entrez = "Human_GOBP_AllPathways_no_GO_iea_April_01_2020_entrezgene.gmt",
#   Hs.symbol = "Human_GOBP_AllPathways_no_GO_iea_April_01_2020_symbol.gmt",
#   Mm.entrez = "Mouse_GOBP_AllPathways_no_GO_iea_April_01_2020_entrezgene.gmt",
#   Mm.symbol = "Mouse_GOBP_AllPathways_no_GO_iea_April_01_2020_symbol.gmt"
# )
#
# pathway.list <- list()
# for (i in 1:length(file.pathways)){
#
#   df.pathway.2 <- qusage::read.gmt(paste0(directory, file.pathways[[names(file.pathways)[i]]]))
#   pathways <- df.pathway.2
#   names(pathways) <- gsub("%.*", "", names(pathways))
#
#   pathway.list[[names(file.pathways)[i]]] <- pathways
#
# }
#
# baderPathways <- pathway.list
#
# output.dir <- "D:/Users/Nick/Dropbox/PDF Projects - JM/R Packages/scMiko/data/"
#
# save(baderPathways, file=getLoadPath("baderPathways.rda", output.dir))
}

Format

A list of pathways

Examples

data(baderPathways)

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.