semvec/pypi-packages huggingface dataset:
napari-imcreg 0.2.1
Control point-based coordinate transformation for Imaging Mass Cytometry (IMC)
License: MIT
Requires Python: >=3.6

# napari-imcreg

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Control point-based coordinate transformation for Imaging Mass Cytometry (IMC)

----------------------------------

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

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## Installation

You can install `napari-imcreg` via [pip]:
```shell
pip install napari-imcreg
```

As napari is in active development, the use of virtual environments is strongly recommended.

## Usage

To start `napari-imcreg` from command line:

```shell
napari-imcreg
```

## Contributing

Contributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.

## License

Distributed under the terms of the [MIT] license,
"napari-imcreg" is free and open source software

## Issues

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

[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
[file an issue]: https://github.com/BodenmillerGroup/napari-imcreg/issues
[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
haplotype-plot 1.1.3
Generates haplotype plots from VCF files.
License: MIT
Requires Python: >=3

# Haplotype plot

Generates haplotype plots for VCF files.
**Requires Python 3 to run**.

[![Build Status](https://travis-ci.org/neobernad/haplotype_plot.svg?branch=master)](https://travis-ci.org/neobernad/haplotype_plot)
[![codecov](https://codecov.io/gh/neobernad/haplotype_plot/branch/master/graph/badge.svg)](https://codecov.io/gh/neobernad/haplotype_plot)

# Pypi

You may install haplotype plot from pip:

```bash
pip install haplotype-plot
```

# Usage

```bash
usage: main.py [-h] -v VCF [-o OUTPUT] -c CHR -p PARENTAL [--phase]
               [--version] [-z {HOM,HET}] [--conf KEY=VALUE [KEY=VALUE ...]]

Creates a haplotype plot from a VCF file

optional arguments:
  -h, --help            show this help message and exit
  -v VCF, --vcf VCF     path to the input sorted VCF file
  -o OUTPUT, --output OUTPUT
                        path to the output PNG haplotype plot file
  -c CHR, --chr CHR     chromosome to plot from the VCF
  -p PARENTAL, --parental PARENTAL
                        sample name from the VCF used as parental haplotype
  --phase               if specified, it will phase the genotypes. An output
                        VCF with the phased genotypes is created
  --version             show program's version number and exit
  -z {HOM,HET}, --zygosis {HOM,HET}
                        zygosis of the input VCF file
  --conf KEY=VALUE [KEY=VALUE ...]
                        set a number of key-value pairs to modify the default
                        plot configuration (do not put spaces before or after
                        the = sign). If a value contains spaces, you should
                        define it with double quotes: foo="this is a
                        sentence". Possible values are: 'start=integer',
                        'end=integer', 'show=boolean', 'xtickslabels=boolean',
                        'size_y=float'
```

For examples of use please go to the [documentation](https://neobernad.github.io/haplotype_plot/#/).

---