PATHway

PATHway is an R package for performing Gene Set Enrichment Analysis (GSEA) and visualizing the results.

Installation

To install the latest version of PATHway directly from GitHub, you can use the devtools package: GitHub with:

1. Install the required Bioconductor packages, clusterProfiler (https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html), org.Hs.eg.db (https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html), enrichplot(https://bioconductor.org/packages/release/bioc/html/enrichplot.html) need to be download by BiocManager. :

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("clusterProfiler")
BiocManager::install("org.Hs.eg.db")
BiocManager::install("enrichplot")

# Install devtools if you haven't already
if (!requireNamespace("devtools", quietly = TRUE)) {
  install.packages("devtools")
}

devtools::install_github("wang-ziyin1997/PATHway")

Usage

After installing the package, you can load it using library(PATHway).

Example

This is a basic example which shows you how to solve a common problem:

library(PATHway)
DEGsData <- PATHway::DEGsData(Yourfilepath, EntrezID=EntrezID, log2FC=log2FoldChange)
GSEAres <- PATHway::GSEAnalysis(DEGsData,Youroutpath)
PATHway::GSEA_histogram(GSEAres,Youroutpath)
PATHway::GSEA_bubble(GSEAres,Youroutpath)

Use test csv to test the code.

library(PATHway)
test_file <- system.file("extdata", "test_data.csv", package = "PATHway")
DEGs <- DEGsData(file = test_file, EntrezID = "EntrezID", log2FC = "log2FoldChange")
GSEAres <- PATHway::GSEAnalysis(DEGs,Youroutpath)
PATHway::GSEA_histogram(GSEAres,Youroutpath)
PATHway::GSEA_bubble(GSEAres,Youroutpath)