GSAO

Gene Set Annotation Overlap

This is a data analysis package allowing the user with a list of genes of interest to find enriched annotations of gene sets from MSigDB C7.

Installation

To install this package, run:

# install.packages("remotes")
remotes::install_github("AhmedMehdiLab/GSAO")

Usage

To use the package, run:

library(GSAO)
genes <- "GENE1 GENE2 GENE3"       # a gene list separated by spaces or commas
input <- process_input_text(genes) 
results <- compute(input)

Statistically enriched annotations are stored in a tidyverse tibble, and can be viewed with:

results$stats

Roxygen documentation is available for all functions.

Notes

You will be asked to give the path for MSigDB XML file. Please drag the XML file to R console to get the path or alternatively write the path:

Example: ~/Downloads/msigdb_v7.5.1_files_to_download_locally/msigdb_v7.5.1.xml

To run it for gene list, please provide the gene names or gene names;

input <- process_input_text("IL1B	EGR3	EGR2	CCR1	PTGS2	SLC25A29	RAB12	CXCL1	FOSB	SFRS15	SGK	FRAT2	TRIB1	NGLY1	THOC7	FPRL1	SFRS2IP	TAX1BP1	FLJ42008	GPR109B	TREM1	MAFB	BTBD14A")

results <- compute(input)
head(results$stats)
head(results$matches)

For single-cell RNAseq, please provide object processed through Seurat pipeline (normalization, scaling, clustering etc performed. With also a label “grp” indicating the group information.

input_Seurat_object <- readRDS(‘Your Path to Seurat RDS File’)

with input_Seurat_object$seurat_clusters containing the seurat clusters to perform differential expression analyses needed in downstream analyses.