This project contains the package tar tar file, manual and vignette for the R package PloGO2, which helps with gene ontology and pathway analysis for multi-condition experiments. The package has been submitted to Bioconductor and is currently under review.
PloGO2_R_Package
This project contains the package tar tar file, manual and vignette for the R package PloGO2, which helps with gene ontology and pathway analysis for multi-condition experiments. The package has been submitted to Bioconductor and is currently under review.
Dependencies
R version > 4.0
Installation
First install dependencies
install.packages(c(‘httr’, ‘openxlsx’, ‘xtable’,’heatmap3’))
if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”)
BiocManager::install(“GOstats”)
BiocManager::install(“GO.db”)
BiocManager::install(“clusterProfiler”)
Next install PloGO2
From within R install from zipfile, using the file PloGO2_1.3.1.tar.gz
Testing
The example script for testing can be found in the script package folder
source(file.path(system.file(“script”, package=”PloGO2”), “plogo2_script.R”))
Optional - use with the WGCNA workflow
BiocManager::install(“impute”)
BiocManager::install(“preprocessCore”)
install.packages(‘WGCNA’)
Test the WGCNA workflow
source(file.path(system.file(“script”, package=”PloGO2”), “WGCNA_proteomics.R”))
Example data
Three datasets in our paper are included in the example data folder.
Pathway database
KEGG pathway databases are available in the pathway DB folder for three common species: human, mouse and arabidopsis.