liz-is / scenicplus Goto Github PK

View Code? Open in Web Editor NEW

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.

License: Other

Python 3.02% Jupyter Notebook 96.97% Dockerfile 0.02%

scenicplus's Introduction

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+:

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.