# scenicplus

**Repository Path**: joyeric_admin_admin/scenicplus

## Basic Information

- **Project Name**: scenicplus
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: main
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2026-04-15
- **Last Updated**: 2026-04-15

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

![alt text](docs/images/SCENIC+_Logo_v5.png "SCENIC+")
[![Documentation Status](https://readthedocs.org/projects/scenicplus/badge/?version=development)](https://scenicplus.readthedocs.io/?badge=main)


# 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](https://scenicplus.readthedocs.io/en/latest/Perturbation_simulation.html#Tutorial:-Perturbation-simulation)

> [!TIP]
> We did a live webinar on using the SCENIC+ workflow. You can rewatch it on [YouTube](https://www.youtube.com/watch?v=QW63LLd1XC8)

## Documentation 

Extensive documentation and tutorials are available at [read the docs](https://scenicplus.readthedocs.io/).

## Installing

To install SCENIC+ (in a Linux environment):

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

```bash

$ 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](https://doi.org/10.1038/s41592-023-01938-4)

## license

The SCENIC+ [license](https://github.com/aertslab/scenicplus/blob/main/LICENCE.txt) covers [SCENIC+](https://github.com/aertslab/scenicplus), [pycisTarget](https://github.com/aertslab/pycistarget), [pycisTopic](https://github.com/aertslab/pycisTopic) and the [cisTarget dabases](https://resources.aertslab.org/cistarget/).