pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
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 .
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
To check your pycisTopic version:
import pycisTopic
pycisTopic.__version__
Tutorials & documentation **********************
Tutorial and documentation are available at https://pycistopic.readthedocs.io/.
- 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.