figeno 1.1.0

Package for generating genomics figures.

figeno

Tool for making genomics figures.

Example figures generated with figeno. Left: allele-specific methylation with nanopore data. Right: HiC data across a structural rearrangement.

Features

• Large collection of tracks (bigwig, HiC, alignments, copy number, SV…)
• Graphical user interface
• Multi-region figures with interactions across regions
• Highlight regions of interest
• Output figures in svg, pdf, eps or png

Quick start

Linux, MacOS

In an environment with python>=3.7:

pip install figeno
figeno gui

This will install figeno and run the graphical user interface (GUI). From the GUI, you can configure the figure and generate it, as well as save the JSON config file which fully defines the figure. The GUI is optional and you can instead use the command line interface: use figeno init to initialize a config file, edit the config file manually, and generate the figure with figeno make.

Windows

Download figeno_windows.zip from https://github.com/CompEpigen/figeno/releases/latest, unzip it and launch the graphical user interface by executing figeno.exe.

Documentation

For more information on how to use figeno, please read the documentation at: https://figeno.readthedocs.io/en/latest/

Test data

Example input files to test figeno are provided in 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 or to contact me directly.