OmicPath: an R package for gene set analysis and pathway network analysis

Installation

library(devtools)
install_github("CBIIT-CGBB/OmicPath")

Examples:

Perform gene set analysis (GSA)

set.seed(1234);
## get some genes from biosystems database of NCBI
dat   <- read.table(system.file("extdata/biosystems_hs.txt", package = "OmicPath"));
genes <- sample(dat[,1], 200);

## select databases (GO) from the package
db  <- db_names()[1];
## do GSA
out <- doGSEA(db=db, gene=genes, filter.num=2, fdr=T);

Map gene information on the pathway

code

Extract gene relationships in the pathway and plot the pathway as network clusters

KEGG: Ras signaling pathway

R codes

Construct networks by gene neighborhoods in the pathway

KEGG: Ras signaling pathway: construct networks by the genes ("PAK2", "BAD", "RASGRF1", "RAP1A", "NRAS", "HRAS", "TIAM1", "RRAS2", "KRAS", "SHC3") and their neighborhoods. The networks contain genes with the neighborhood order = 1 and 2. The seed genes were colored in red.

R codes (order=1)

R codes (order=2)

Additional examples: cluster algorithms in igraph

R codes