Introduction Base omix env task Base r env task Blast ec list extractor Blast to EC-number Annotator Deep ec Deep ec env task Deep ec list extractor DESeq2 pairwise differential analysis ECListMerger Feature Counts Genome by mapping assembly pipeline Gmap align gtf Gmap index GSEA_GO_enrichment HTSeqCount Inter pro scan env task Py gsea env task Salmon index Salmon quant mapping Star index Star mapping genome reads Star mapping transcriptome reads Subread env task Top go2 env task TopGO2_GO_enrichment Trim fq env task TrimGalore cleaning Version
Technical Documentation
Resources
Tasks
GSEA_GO_enrichment
Performs GO term enrichment using pyGSEA library
GseaGoTerm class.
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
Input
Output
Configuration
Top_results_number
Number of the best enriched GO term to include in the top list
int
10
Threads
Number of threads
int
2