Metadata-Version: 2.1
Name: infercnvpy
Version: 0.4.2
Summary: Infercnv is a scalable python library to infer copy number variation (CNV) events from single cell transcriptomics data. It is heavliy inspired by InferCNV, but plays nicely with scanpy and is much more scalable.
Project-URL: Documentation, https://infercnvpy.readthedocs.io/
Project-URL: Source, https://github.com/icbi-lab/infercnvpy
Project-URL: Home-page, https://github.com/icbi-lab/infercnvpy
Author: Gregor Sturm
Maintainer-email: Gregor Sturm <gregor.sturm@i-med.ac.at>
License: BSD 3-Clause License
        
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License-File: LICENSE
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Requires-Dist: pycairo>=1.20; sys_platform == 'win32'
Requires-Dist: pyreadr
Requires-Dist: pytoml
Requires-Dist: scanpy>=1.6.0
Requires-Dist: session-info
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Provides-Extra: copykat
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Description-Content-Type: text/markdown

# infercnvpy: Scanpy plugin to infer copy number variation (CNV) from single-cell transcriptomics data

[![Tests][badge-tests]][link-tests]
[![Documentation][badge-docs]][link-docs]
[![PyPI][badge-pypi]][link-pypi]

[badge-tests]: https://img.shields.io/github/actions/workflow/status/grst/infercnvpy/test.yaml?branch=main
[link-tests]: https://github.com/icbi-lab/infercnvpy/actions/workflows/test.yml
[badge-docs]: https://img.shields.io/readthedocs/infercnvpy
[badge-pypi]: https://img.shields.io/pypi/v/infercnvpy?logo=PyPI
[link-pypi]: https://pypi.org/project/infercnvpy/

Infercnv is a scalable python library to infer copy number variation (CNV) events from single cell transcriptomics data. It is heavliy inspired by [InferCNV][], but plays nicely with [scanpy][] and is much more scalable.

[infercnv]: https://github.com/broadinstitute/inferCNV/wiki
[scanpy]: https://scanpy.readthedocs.io/en/stable/index.html

![The main result of infercnv](img/infercnv_heatmap.png)

**WARNING**:

**This package is still experimental. The results have not been validated,
except in that they look similar, but not identical, to the results of InferCNV.**

**We are happy about feedback and welcome contributions!**

## Getting started

Please refer to the [documentation][link-docs]. In particular, the

-   [API documentation][link-api].

## Installation

You need to have Python 3.8 or newer installed on your system. If you don't have
Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).

There are several alternative options to install infercnvpy:

1. Install the latest release of `infercnvpy` from `PyPI <https://pypi.org/project/infercnvpy/>`\_:

```bash
pip install infercnvpy
```

2. Install the latest development version:

```bash
pip install git+https://github.com/icbi-lab/infercnvpy.git@main
```

To (optionally) run the `copyKAT` algorithm, you need a working R installation
and the [copykat][] package installed. Usually, if `R` is in your `PATH`, [`rpy2`][rpy2] automatically
detects your R installation. If you get an error message while importing `infercnvpy`,
try setting the `R_HOME` environment variable before importing infercnvpy:

```python
import os

os.environ["R_HOME"] = "/usr/lib/R"
import infercnvpy
```

[copykat]: https://github.com/navinlabcode/copykat#step-1-installation
[rpy2]: https://rpy2.github.io/

## Release notes

See the [changelog][changelog].

## Contact

For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].
If you found a bug, please use the [issue tracker][issue-tracker].

## Citation

n/a

[scverse-discourse]: https://discourse.scverse.org/
[issue-tracker]: https://github.com/icbi-lab/infercnvpy/issues
[changelog]: https://infercnvpy.readthedocs.io/latest/changelog.html
[link-docs]: https://infercnvpy.readthedocs.io
[link-api]: https://infercnvpy.readthedocs.io/latest/api.html
