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.

[!NOTE]
Updates:

August 30th 2024: Perturbation simulation got updated, please find tutorial here

[!TIP] We did a live webinar on using the SCENIC+ workflow. You can rewatch it on YouTube

Documentation

Extensive documentation and tutorials are available at read the docs.

Installing

To install SCENIC+ (in a Linux environment):

We highly recommend to install SCENIC+ in a new conda environment.

$ conda create --name scenicplus python=3.11 -y
$ conda activate scenicplus
$ git clone https://github.com/aertslab/scenicplus
$ cd scenicplus
$ pip install .

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. (2023). SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

license

The SCENIC+ license covers SCENIC+, pycisTarget, pycisTopic and the cisTarget dabases.