vreuter / hicognition

A visual exploration and hypothesis testing tool for 3D genomics

HiCognition: A visual exploration and hypothesis testing tool for 3D genomics

HiCognition is a data exploration tool that allows stream-lined exploration of aggregate genomic data. HiCognition is centered around Hi-C data but also enables integration of Chip-seq and region-based data.

HiCognition implements the region-set focus approach, a concept that allows exploration of genomic region sets. For more details see the concepts section of our documentation.

Get started

To get started using HiCognition, check out the quickstart section of our documentation.

Installation

If you want to set-up a HiCognition instance yourself, check out the installation section of our documentation. An optional CLI tool to interface with the web API can be found in the HiCognition library repository.

Development

If you want to contribute to HiCognition, be sure to read the development section or our documentation.

Citing

Langer, C. C. H.^*, Mitter, M.^*, Stocsits, R. R. & Gerlich, D. W. (2022) HiCognition: a visual exploration and hypothesis testing tool for 3D genomics. bioRxiv doi:10.1101/2022.04.30.490134

^* equal contribution

@article {HiCognition2022,
	author = {Langer, Christoph C. H. and Mitter, Michael and Stocsits, Roman R. and Gerlich, Daniel W},
	title = {HiCognition: a visual exploration and hypothesis testing tool for 3D genomics},
	year = {2022},
	doi = {10.1101/2022.04.30.490134},
	URL = {https://www.biorxiv.org/content/early/2022/05/01/2022.04.30.490134},
	journal = {bioRxiv}
}

If you want to contribute to HiCognition, be sure to read the development section or our documentation.

Showcase version

A demo version with disabled preprocessing but all of the sessions used for the figures of the manuscript can be found on our homepage.