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# figeno

Tool for making genomics figures.
```
FIGENO is a
FIGure
GENerator
for GENOmics
```
With figeno, you can plot various types of sequencing data along genomic coordinates.

![figeno](docs/content/images/figeno.png)
Example figures generated with figeno. Left: allele-specific methylation with nanopore data. Right: HiC data across a structural rearrangement.
Example figures generated with figeno. Left: allele-specific methylation with nanopore data. Right: HiC data across a structural rearrangement. See more examples [here]()

## Features
- Large collection of tracks (bigwig, HiC, alignments, copy number, SV…)
- Graphical user interface
- Large collection of tracks (bigwig, HiC, alignments with base modifications, WGS with copy numbers and SV…)
- Multi-region figures with interactions across regions
- Highlight regions of interest
- Output figures in svg, pdf, eps or png
- Graphical user interface, command line interface and python API
- Output figures in vector graphics (svg, pdf) or bitmap (png)

## Quick start
### Linux, MacOS
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## Test data
Example input files to test figeno are provided in [test_data](https://github.com/CompEpigen/figeno/tree/main/test_data).

## Bugs and improvements
If you encounter a bug or would like to have a new feature added, please do not hesitate to [raise an issue](https://github.com/CompEpigen/figeno/issues/new) or to [contact me directly](https://www.dkfz.de/en/CanEpi/staff/kontakt/Sollier_Etienne.php).
## Feedback
If you encounter a bug or would like to have a new feature added, please do not hesitate to [raise an issue](https://github.com/CompEpigen/figeno/issues/new) or to [contact me directly](https://www.dkfz.de/en/CanEpi/staff/kontakt/Sollier_Etienne.php). You can also provide feedback by completing this [anonymous form](https://forms.gle/xb9Ygk6zsJCJUQYm9), which would help me improve figeno!

## Citation
If you use figeno in your research, we would appreciate it if you would cite the manuscript describing figeno:

Etienne Sollier, Jessica Heilmanm, Clarissa Gerhauser, Michael Scherer, Christoph Plass, Pavlo Lutsik. Figeno: multi-region genomic figures with long-read support. [doi:10.1101/2024.04.22.590500](https://doi.org/10.1101/2024.04.22.590500).
Etienne Sollier, Jessica Heilmann, Clarissa Gerhauser, Michael Scherer, Christoph Plass, Pavlo Lutsik. Figeno: multi-region genomic figures with long-read support. [doi:10.1101/2024.04.22.590500](https://doi.org/10.1101/2024.04.22.590500).

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