SCENIC+ single-cell eGRN inference
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 ipython3Check 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.