napari-kics

A plugin to estimate chromosome sizes from karyotype images.


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    Source code:

    • Information not submitted

    napari-kics

    standard-readme compliant License PyPI Python Version Python package

    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

    Version:

    • 0.0.3rc6

    Release date:

    • 22 May 2022

    First released:

    • 02 May 2022

    License:

    • BSD-3-Clause

    Supported data:

    • Information not submitted

    GitHub activity:

    • Stars: 0
    • Forks: 0
    • Issues + PRs: 0

    Python versions supported:

    Operating system:

    Requirements:

    • napari-plugin-engine (>=0.1.4)
    • numpy
    • napari[all]
    • scikit-image
    • pandas
    • pulp
    • pyqtgraph

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