Performs GO term enrichment using pyGSEA library
A class that wraps the PyGSEA library for performing Gene Set Enrichment Analysis (GSEA) on gene list data.
PyGSEA is an open-source Python library for performing gene set enrichment analysis using various databases of gene sets, including the Gene Ontology (GO) database.
More information here: https://github.com/zqfang/gseapy
[Mandatory]: - Gene list file must contains genes, one per line.
- The Gene Matrix Transposed (GMT) file format, also known as gene univers file which is a tab-delimited text file format where each row represents a gene set, and the first column is the name of the gene set, followed by a description, and then a list of genes that belong to that set.
Here's are examples of a GMT file and Gene list file for performing GO term enrichment analysis:
- Gene list files : Gene_0102 Gene_0708 ... Gene_0909 - Gene universe file (tab separated) : # Gene ontology enrichment analysis Gene_0001 NA GO:0008150 GO:0009987 GO:0016192 GO:0050896 Gene_0002 Here is a description of the gene GO:0008150 GO:0009987 Gene_0003 NA GO:0050896 ... Gene_2305 NA
Number of the best enriched GO term to include in the top list
Number of threads