Installation

Environment Setting

It is highly recommended to use the conda virtual environment to install this package. After installation of conda, create a virtual environment for PySNAIL using the following command:

$ conda create -n pysnail python=3.7.7
$ conda activate pysnail

Install Package

Download the source code from git@github.com:kuijjerlab/PySNAIL.git and install the package using pip:

$ git clone git@github.com:kuijjerlab/PySNAIL.git
$ cd PySNAIL
$ pip install -e .

To reproduce the analysis we provide in the manuscript:

$ git clone git@github.com:kuijjerlab/PySNAIL.git
$ cd PySNAIL
$ conda activate pysnail
$ conda config --add channels anaconda
$ conda config --add channels defaults
$ conda config --add channels bioconda
$ conda config --add channels conda-forge
$ conda config --add channels bokeh
$ conda install --file conda_requirement.txt
$ pip install -r pip_requirement.txt
$ pip install -e .

Example Dataset

The PySNAIL packages includes an example dataset for users to test the method on. This can be found under the sample_data directories. The expression.tsv contains 10,000 randomly selected genes from the Mouse ENCODE Project Consortium. The groups.tsv contains the tissue information for each sample.

$ sample_data/expression.tsv
$ sample_data/groups.tsv