napari-kics

A plugin to estimate chromosome sizes from karyotype images.

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

Table of Contents

• Install
• Usage
• Example
• Citation
• License
• Issues
• Contributing

Install

napari →

Install KICS with Plugins → Install/Uninstall Plugins…, enter KICS into the search field and install the plugin.

pip →

You can install napari-kics via pip:

pip install napari-kics

conda →

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. bioRxiv. DOI: 10.1101/2022.05.22.492982.

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

plugin_overview.mp4