Installation

Stable release

PyPI

To install pertpy, run this command in your terminal:

pip install pertpy

This is the preferred method to install pertpy, as it will always install the most recent stable release. If you don’t have pip installed, this Python installation guide can guide you through the process.

conda-forge

Alternatively, you can install pertpy from conda-forge:

conda install -c conda-forge pertpy

Additional dependency groups

Differential gene expression interface

The DGE interface of pertpy requires additional dependencies that can be installed by running:

pip install pertpy[de]

Note that edger in pertpy requires edger and rpy2 to be installed:

BiocManager::install("edgeR")

pip install rpy2

milo

milo requires either the “de” extra for the “pydeseq2” solver:

pip install 'pertpy[de]'

or, edger, statmod, and rpy2 for the “edger” solver:

BiocManager::install("edgeR")
BiocManager::install("statmod")

pip install rpy2

tascCODA

TascCODA requires an additional set of dependencies (ete4, pyqt6, and toytree) that can be installed by running:

pip install pertpy[tcoda]

From sources

The sources for pertpy can be downloaded from the Github repo.

You can either clone the public repository:

$ git clone git://github.com/scverse/pertpy

Or download the tarball:

$ curl -OJL https://github.com/scverse/pertpy/tarball/master