HiCognition is an implementation of the region-set focus approach. One central aspect of the application is to allow the management of datasets, both representing genomic regions and features. For more complex analyses, HiCognition also implements managing collections of datasets.
This chapter describes genomic regions are the central element region-set focus approach in more detail.
Genomic features are mainly used to understand genomic regions in the region-set focus approach. They can thus be thought of as “independent variables” that explain the “dependent” genomic regions.
HiCognition uses collections to group datasets together for them to be available for some of the more complex processing algorithms.
HiCognition allows managing genome assemblies to work with different assemblies and organisms in parallel. This chapter describes how this is done.