ken-lau-lab / nvr

NVR is a python implementation of gene feature selection used in Welch et al.,2016

NVR (neighborhood variance ratio)

Python implementation of NVR (neighborhood variance ratio) gene selection to select genes with local and monotonic variation (Welch et al., 2016). The selected genes possess specific expression patterns over the entire data space amenable to trajectory analysis. Support for python 2 is now deprecated with version 0.1.0 scanpy integration, as scanpy requires python 3.

Installation for Mac or Linux

NVR requires igraph and scanpy for operation, so please see our instructions for the installation of these packages.

There are two ways to install NVR with Mac/Linux operating systems.

git clone git://github.com/KenLauLab/NVR
cd NVR
pip install .

pip install nvr #this needs to be updated so avoid doing this for now

Installation for Windows (in Anaconda3 environment)

In your anaconda terminal, navigate to a directory where you want to install NVR (e.g. d:\src)

cd d:\src
git clone git://github.com/KenLauLab/NVR
cd NVR
pip install .

Tutorial

Please see the NVR running .ipynb tutorial as well as its associated dataset