Tutorials¶
Worked examples as Jupyter notebooks, shown with their saved outputs. Each one is in the notebooks directory of the repository, ready to run.
- Do enrichment analyses using the Human Phenotype Ontology (HPO)
- Loading the optional definition attribute
- Calculating Annotation Coverage
- Reading Annotations from a GO Association File (GAF)
- Reading a Gene Product Association Data (GPAD) file
- Annotations in NCBI’s gene2go file
- How to download background genes from NCBI
- Cell Cycle genes
- How to traverse to GO children and descendants
- Information Content for Custom GO Annotations (id2go format)
- How to get Descendants Count and Information Content
- How to get GO IDs up both the ‘is a’ and ‘part of’ relationships
- Loading obsolete GO terms
- Run a Gene Ontology Enrichment Analysis (GOEA)
- Run a GOEA. Print study genes as either IDs symbols
- Gene Ontology Enrichment Analysis (GOEA)
- Group Significant GO terms by Frequently Seen Words
- How to extract information from parent GO terms
- How to traverse to GO parents and ancestors
- Adding optional relationships changes the dcnt value
- Relationships in the GO
- Report counts of GO terms at various levels and depths
- Computing basic semantic similarities between GO terms
- Calculating Wang’s Semantic Similarity between two GO Terms
- Notebook Images
- GO parents