FAQ

What type of enrichment analysis does gokit perform?

gokit performs overrepresentation analysis (ORA) using Fisher’s exact test. It tests whether GO terms are significantly enriched (overrepresented) or depleted (underrepresented) in a study gene set compared to a background population.

What association file formats does gokit support?

gokit supports four association file formats: id2gos (simple gene-to-GO mapping), GAF (Gene Association File format 2.x), GPAD (Gene Product Association Data format 1.x/2.x), and NCBI gene2go format. By default, gokit automatically detects the format.

What multiple testing correction methods are available?

gokit supports the following correction methods: Benjamini-Hochberg FDR (fdr_bh, default), Benjamini-Yekutieli FDR (fdr_by), Bonferroni (bonferroni), Holm (holm), and no correction (none).

What semantic similarity metrics are supported?

gokit supports Jaccard index, Resnik similarity (based on information content of the most informative common ancestor), Lin similarity, and Wang similarity for comparing GO term sets across studies.

Does gokit have any dependencies?

gokit is designed with zero core dependencies for maximum portability. Optional extras include pyarrow for Parquet output (pip install gokit[io]) and matplotlib/networkx for plotting (pip install gokit[plot]).

How do I download the Gene Ontology files?

Use the gokit download command to download go-basic.obo and goslim_generic.obo into the current directory. Alternatively, download them manually from http://current.geneontology.org/ontology/.

I am having trouble installing gokit, what should I do?

Please install gokit using a virtual environment as directed in the installation instructions. If you are still running into issues after installing in a virtual environment, please open an issue on GitHub.

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