categoryCompare: A Flexible Framework for Enrichment of Feature Annotations and Their Comparisons

We have recently released a series of improvements to the next version of categoryCompare, a flexible framework for enrichment of feature annotations and comparisons between enrichment of annotations across two or more experimental groups.

First, we have added the ability to use any type of gene or feature annotation. This means that enrichments can be calculated for any grouping of genes that can be generated by other means, including those from the Gene Ontology (GO), KEGG and Reactome pathways, groupings of GO terms such as those generated by GOCats [1], and from protein-protein interaction neighborhoods.

Second, we have added methods that facilitate conversions from feature-annotation lists provided by users to the annotation objects used internally by categoryCompare.

Third, we have created command-line executables for each stage of the typical categoryCompare analysis, which enable the use of categoryCompare by non-R programmers as well as interoperability with other tools and workflows.

These improvements are available in version 2 of categoryCompare on GitHub at https://github.com/rmflight/categoryCompare2.