| Name | infercnvpy JSON |
| Version |
0.5.0
JSON |
| download |
| home_page | None |
| 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. |
| upload_time | 2024-06-26 12:15:09 |
| maintainer | None |
| docs_url | None |
| author | Gregor Sturm |
| requires_python | >=3.10 |
| license | BSD 3-Clause License Copyright (c) 2022, Gregor Sturm All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| keywords |
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| VCS |
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| bugtrack_url |
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No requirements were recorded.
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# 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/icbi-lab/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
**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 3.10 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/en/latest/api.html
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"description": "# infercnvpy: Scanpy plugin to infer copy number variation (CNV) from single-cell transcriptomics data\n\n[![Tests][badge-tests]][link-tests]\n[![Documentation][badge-docs]][link-docs]\n[![PyPI][badge-pypi]][link-pypi]\n\n[badge-tests]: https://img.shields.io/github/actions/workflow/status/icbi-lab/infercnvpy/test.yaml?branch=main\n[link-tests]: https://github.com/icbi-lab/infercnvpy/actions/workflows/test.yml\n[badge-docs]: https://img.shields.io/readthedocs/infercnvpy\n[badge-pypi]: https://img.shields.io/pypi/v/infercnvpy?logo=PyPI\n[link-pypi]: https://pypi.org/project/infercnvpy/\n\nInfercnv 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.\n\n[infercnv]: https://github.com/broadinstitute/inferCNV/wiki\n[scanpy]: https://scanpy.readthedocs.io/en/stable/index.html\n\n\n\n**WARNING**:\n\n**This package is still experimental. The results have not been validated,\nexcept in that they look similar, but not identical, to the results of InferCNV.**\n\n**We are happy about feedback and welcome contributions!**\n\n## Getting started\n\nPlease refer to the [documentation][link-docs]. In particular, the\n\n- [API documentation][link-api].\n\n## Installation\n\nYou need to have Python 3.10 or newer installed on your system. If you don't have\nPython installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).\n\nThere are several alternative options to install infercnvpy:\n\n1. Install the latest release of `infercnvpy` from `PyPI <https://pypi.org/project/infercnvpy/>`\\_:\n\n```bash\npip install infercnvpy\n```\n\n2. Install the latest development version:\n\n```bash\npip install git+https://github.com/icbi-lab/infercnvpy.git@main\n```\n\nTo (optionally) run the `copyKAT` algorithm, you need a working R installation\nand the [copykat][] package installed. Usually, if `R` is in your `PATH`, [`rpy2`][rpy2] automatically\ndetects your R installation. If you get an error message while importing `infercnvpy`,\ntry setting the `R_HOME` environment variable before importing infercnvpy:\n\n```python\nimport os\n\nos.environ[\"R_HOME\"] = \"/usr/lib/R\"\nimport infercnvpy\n```\n\n[copykat]: https://github.com/navinlabcode/copykat#step-1-installation\n[rpy2]: https://rpy2.github.io/\n\n## Release notes\n\nSee the [changelog][changelog].\n\n## Contact\n\nFor questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].\nIf you found a bug, please use the [issue tracker][issue-tracker].\n\n## Citation\n\nn/a\n\n[scverse-discourse]: https://discourse.scverse.org/\n[issue-tracker]: https://github.com/icbi-lab/infercnvpy/issues\n[changelog]: https://infercnvpy.readthedocs.io/latest/changelog.html\n[link-docs]: https://infercnvpy.readthedocs.io\n[link-api]: https://infercnvpy.readthedocs.io/en/latest/api.html\n",
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