napari-kics

A plugin to estimate chromosome sizes from karyotype images.

This napari plugin was generated with Cookiecutter using with @napari's cookiecutter-napari-plugin template.

Table of Contents¶

• Install
• Usage
• Example
• Citation
• Maintainer
• Contributing
• License

Install¶

You can install napari-kics via pip:

pip install napari-kics

This will install all required dependencies as well. We recommend installing it in a virtual environment, e.g. using conda:

conda create -n kics python
conda activate kics
pip install napari-kics

We recommend using mamba as a faster alternative to conda.

Usage¶

1. Launch Napari via command line (napari).
2. Activate the plugin via menu Plugins -> napari-kics: Karyotype Widget.
3. Select file via File -> Open File.
4. Follow instructions in the panel on the right.

You may use the interactive analysis plots directly via command line:

karyotype-analysis-plots

Example¶

1. Launch Napari via command line (napari).
2. Activate the plugin via menu Plugins -> napari-kics: Karyotype Widget.
3. Select file via File -> Open Sample -> napari-kics: sample.
4. Follow instructions in the panel on the right.

Try out the interactive analysis plots directly via command line:

karyotype-analysis-plots --example

Citation¶

Arne Ludwig, Alexandr Dibrov, Gene Myers, Martin Pippel. Estimating chromosome sizes from karyotype images enables validation of de novo assemblies. To be published.

License¶

Distributed under the terms of the BSD-3 license, "napari-kics" is free and open source software

Issues¶

If you encounter any problems, please file an issue along with a detailed description.

Contributing¶

Contributions are very welcome. Please file a pull request with your contribution.

You can setup a local development environment for napari-kics via pip:

git clone https://github.com/mpicbg-csbd/napari-kics.git
cd napari-kics
pip install -e .

Overview¶