pycisTopic

pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.

Installation

To install pycisTopic:

git clone https://github.com/aertslab/pycisTopic.git
cd pycisTopic
pip install .

Depending on your pip version, you may need to run this pip command instead:

pip install -e .

Creating a Docker/Singularity Image

To build a Docker image, then create a Singularity image from this:

# Clone repositories (pycisTopic and pycistarget)
git clone https://github.com/aertslab/pycisTopic.git
git clone https://github.com/aertslab/pycistarget.git

# Build image
podman build -t aertslab/pycistopic:latest . -f pycisTopic/Dockerfile

# Export to oci
podman save --format oci-archive --output pycistopic_img.tar localhost/aertslab/pycistopic

# Build to singularity
singularity build pycistopic.sif oci-archive://pycistopic_img.tar

# Add all binding paths where you would need to access
singularity exec -B /lustre1,/staging,/data,/vsc-hard-mounts,/scratch pycistopic.sif ipython3

Check version

To check your pycisTopic version:

import pycisTopic
pycisTopic.__version__

Tutorials & documentation

Tutorial and documentation are available at https://pycistopic.readthedocs.io/.

Questions?

• If you have technical questions or problems, such as bug reports or ideas for new features, please open an issue under the issues tab.
• If you have questions about the interpretation of results or your analysis, please start a Discussion under the Discussions tab.

Reference

Bravo Gonzalez-Blas, C. & De Winter, S. et al. (2022). SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks