semvec/pypi-packages huggingface dataset:
vivarium-inputs 5.2.6
Transformations and artifact building for the vivarium microsimulation project.

Vivarium Inputs
===============

.. image:: https://badge.fury.io/py/vivarium-inputs.svg
    :target: https://badge.fury.io/py/vivarium-inputs

.. image:: https://github.com/ihmeuw/vivarium_inputs/actions/workflows/build.yml/badge.svg?branch=main
    :target: https://github.com/ihmeuw/vivarium_inputs
    :alt: Latest Version

.. image:: https://readthedocs.org/projects/vivarium_inputs/badge/?version=latest
    :target: https://vivarium_inputs.readthedocs.io/en/latest/?badge=latest
    :alt: Latest Docs


This package is used to transform Global Burden of Disease data and package it into data artifacts
used as inputs into vivarium simulations.

It requires access to the IHME cluster for use (but not for testing).


`Check out the docs! <https://vivarium.readthedocs.io/projects/vivarium-inputs/en/latest/>`_
--------------------------------------------------------------------------------------------
CNVpytor 1.3.2
Python extension of CNVnator

![CNVpytor Logo](https://raw.githubusercontent.com/abyzovlab/CNVpytor/master/cnvpytor/imgs/cnvpytor_w_640.png)

[3D printable CNVpytor logo (stl file)](https://github.com/abyzovlab/CNVpytor/blob/master/imgs/CNVpytor.stl)

# CNVpytor - a python extension of CNVnator

CNVpytor is a Python package and command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads developed in Abyzov Lab, Mayo Clinic.

Follow [CNVpytor Twitter account](https://twitter.com/cnvpytor).


### Citing CNVpytor

CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing
<br />Milovan Suvakov, Arijit Panda, Colin Diesh, Ian Holmes, Alexej Abyzov, GigaScience, Volume 10, Issue 11, November 2021, giab074
[https://doi.org/10.1093/gigascience/giab074](https://doi.org/10.1093/gigascience/giab074)

## Learn how to use CNVpytor in 10 minutes

* [Geting started](https://github.com/abyzovlab/CNVpytor/blob/master/GettingStarted.md) with command line interface
* [Jupyter notebook](https://github.com/abyzovlab/CNVpytor/blob/master/examples/PythonLibraryGuide.ipynb): How to use CNVpytor from Python
* [Google Colab](https://github.com/abyzovlab/CNVpytor/blob/master/examples/Colab.ipynb): With CEPH trio example dataset
* [Video Tutorial](https://www.youtube.com/watch?v=RJMQtrD0SuE): 3-minute YT demo

## Gallery

| | |
|---|---|
| Manhattan plot ([see example](https://github.com/abyzovlab/CNVpytor/blob/master/examples/manhattan.md))| Circular plot ([see example](https://github.com/abyzovlab/CNVpytor/blob/master/examples/circular.md))|
|<img src="https://raw.githubusercontent.com/abyzovlab/CNVpytor/master/imgs/manhattan.png" width="512px">|<img src="https://raw.githubusercontent.com/abyzovlab/CNVpytor/master/imgs/circular.png" width="512px">|
| Region plot ([see example](https://github.com/abyzovlab/CNVpytor/blob/master/examples/region.md))| Compare regions ([see example](https://github.com/abyzovlab/CNVpytor/blob/master/examples/compare.md))|
|<img src="https://raw.githubusercontent.com/abyzovlab/CNVpytor/master/imgs/region.png" width="512px">|<img src="https://raw.githubusercontent.com/abyzovlab/CNVpytor/master/imgs/compare.png" width="512px">|
| Merging and annotating calls ([see example](https://github.com/abyzovlab/CNVpytor/blob/master/examples/merging.md))|Call somatic CNAs ([see example](https://github.com/abyzovlab/CNVpytor/blob/master/examples/JointCaller.md))|
|<img src="https://raw.githubusercontent.com/abyzovlab/CNVpytor/master/imgs/merging.png" width="512px">|<img src="https://raw.githubusercontent.com/abyzovlab/CNVpytor/master/imgs/joint_caller.png" width="512px">


## Install

```
> pip install cnvpytor
> cnvpytor -download
```

## Using

Check [CNVpytor github page](https://github.com/abyzovlab/CNVpytor).

## License

Released under MIT licence.