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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](https://gerlichlab.github.io/hicognition/docs/concepts/) of our documentation.
HiCognition implements the region-set focus approach, a concept that allows exploration of genomic region sets. For more details see the [concepts section](https://hicognition.com/docs/concepts/) of our documentation.

## Get started

To get started using HiCognition, check out the [quickstart section](https://gerlichlab.github.io/hicognition/docs/getting_started/get_started_w_example_data/) of our documentation.
To get started using HiCognition, check out the [quickstart section](https://hicognition.com/docs/getting_started/get_started_w_example_data/) of our documentation.


## Installation

If you want to set-up a HiCognition instance yourself, check out the [installation section](https://gerlichlab.github.io/hicognition/docs/installation/) of our documentation. An optional CLI tool to interface with the web API can be found in the [HiCognition library](https://github.com/gerlichlab/hicognition_lib) repository.
If you want to set-up a HiCognition instance yourself, check out the [installation section](https://hicognition.com/docs/installation/) of our documentation. An optional CLI tool to interface with the web API can be found in the [HiCognition library](https://github.com/gerlichlab/hicognition_lib) repository is under development.

## Development

If you want to contribute to HiCognition, be sure to read the [development section](https://gerlichlab.github.io/hicognition//docs/development/) or our documentation.
If you want to contribute to HiCognition, be sure to read the [development section](https://hicognition.com/docs/development/) or our documentation.

## Citing

Expand All @@ -34,7 +34,7 @@ Langer, C. C. H.<sup>\*</sup>, Mitter, M.<sup>\*</sup>, Stocsits, R. R. & Gerlic

```bibtex
@article {HiCognition2022,
author = {Langer, Christoph C. H. and Mitter, Michael and Stocsits, Roman R. and Gerlich, Daniel W},
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},
Expand All @@ -46,6 +46,6 @@ Langer, C. C. H.<sup>\*</sup>, Mitter, M.<sup>\*</sup>, Stocsits, R. R. & Gerlic

If you want to contribute to HiCognition, be sure to read the [development section](https://gerlichlab.github.io/hicognition/docs/development/) or our documentation.

## Showcase version
## Public server

A demo version with disabled preprocessing but all of the sessions used for the figures of the manuscript can be found on our [homepage](https://hicognition.com/app/).
A demo version with all of the sessions used for the figures of the manuscript can be found on our [homepage](https://app.hicognition.com/). The server has all functionality enabled and users can sign up for a free account using a valid e-mail address to gain fast hands-on experience of HiCognition.
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