README.md

In stephenslab/pathways: Gene Set Enrichment Analysis Using Human and Mouse Gene Sets

pathways

Human and mouse gene sets compiled for gene set enrichment analysis, and a simple interface for performing gene set enrichment analysis using fgsea. The gene sets are compiled from NCBI BioSystems, Pathway Commons and MSigDB. The gene sets are compiled from three sources: NCBI BioSystems, Pathway Commons and MSigDB.

See here for an example of an interactive plot for exploring the results of a gene set enrichment analysis on differential expression in B cells vs. other immune cell populations.

Quick Start

Install the package:

library(remotes)
install_github("stephenslab/pathways")

Load the package:

library(pathways)

Try running the gene set enrichment analysis example (not that it may take a little while to complete the gene set enrichment analysis):

example("perform_gsea")

Other notes

• inst/scripts/prepare_human_gene_set_data.R and inst/scripts/prepare_mouse_gene_set_data.R are the R scripts used to generate the gene set data files.

• inst/code/read_gene_set_data.R contains some functions used in the data preparation scripts.

• See the inst/datafiles directory for data files downloaded from their original sources as well as somethe processed data files. Some of the data files are not actually included in the git repository because they are large; see below for instructions on downloading the data.

• Homo_sapiens.gene_info.gz and Mus_musculus.gene_info.gz are tab-delimited files containing gene information. These files were downloaded from the NCBI FTP site on October 15, 2020.

• bsid2info.gz is a tab-delimited text file containing information about the NCBI BioSystems pathways. This file was downloaded from the NCBI FTP site on March 22, 2020.

• biosystems_gene.gz is a tab-delimited file containing gene set data for the NCBI BioSystems pathways. This file was downloaded from the NCBI FTP site on March 22, 2020.

• PathwayCommons12.All.hgnc.gmt.gz is a tab-delimited text file containing pathway data, including gene sets. This file was downloaded from Pathway Commons on March 20, 2020.

• msigdb_v7.2.xml.gz is an XML file containing information about the MSigDB gene sets. This file was downloaded from here on October 15, 2020. The MSigDB XML format is described here.

stephenslab/pathways documentation built on March 17, 2021, 11:03 p.m.