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 description
infercnvpy: Scanpy plugin to infer copy number variation (CNV) from single-cell transcriptomics data
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.
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. In particular, the
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.
There are several alternative options to install infercnvpy:
- Install the latest release of
infercnvpy
fromPyPI <https://pypi-hypernode.com/project/infercnvpy/>
_:
pip install infercnvpy
- Install the latest development version:
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
automatically
detects your R installation. If you get an error message while importing infercnvpy
,
try setting the R_HOME
environment variable before importing infercnvpy:
import os
os.environ["R_HOME"] = "/usr/lib/R"
import infercnvpy
Release notes
See the changelog.
Contact
For questions and help requests, you can reach out in the scverse discourse. If you found a bug, please use the issue tracker.
Citation
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