SCENIC+ single-cell eGRN inference

Tip

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Note

The code of SCENIC+ has been extensively optmized. We strongly recommend to use the development version of SCENIC+. click here to switch branch!

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.

Documentation

Extensive documentation and tutorials are available at read the docs.

Installing

To install SCENIC+ (in a Linux environment):

git clone https://github.com/aertslab/scenicplus
cd scenicplus
pip install -e .

Creating a Docker/Singularity Image

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

# Clone repositories 
git clone https://github.com/aertslab/pySCENIC.git
git clone https://github.com/aertslab/LoomXpy.git
git clone https://github.com/aertslab/pycisTopic.git
git clone https://github.com/aertslab/pycistarget.git
git clone https://github.com/aertslab/scenicplus.git

# Login
podman login docker.io

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

# Export to oci 
podman save --format oci-archive --output scenicplus_img.tar localhost/aertslab/scenicplus

# Build to singularity
singularity build scenicplus.sif oci-archive://scenicplus_img.tar

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

Check version

To check your SCENIC+ version:

import scenicplus
scenicplus.__version__

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.

References

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