dpeerlab / Symphony

Symphony algorithm for inference of cell type specific gene regulatory networks from scRNA-seq and ATAC-seq

Symphony

Installation

Install Miniconda for Python 3+: https://docs.conda.io/en/latest/miniconda.html

conda create -n SymphonyEnv python=3.6.10 pip
conda activate SymphonyEnv
pip install -r requirements.txt

Running Notebook

jupyter notebook notebooks/SymphonyDemo.ipynb

Input Files for Demo

The input files for running the demo notebook can be accessed here: https://tinyurl.com/yaba9xuq

Symphony is associated with the following publication: Bachireddy, Azizi, et al. Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy, Cell Reports, 2021.

Processed data and more information can be found here: https://sites.google.com/view/tcellsdli