scConGraph is a scalable bi-layer graph model that efficiently integrates cross-time context information, enabling the comprehensive analysis of tumor cell dynamic responses from paired perturbed or time-seiries single-cell transcriptomics.

scConGraph is currently available for Linux systems because the embedding method we use, LINE, is implemented for Linux. If you use the visualization methods in scConGraph, which are implemented in Python, there are no system restrictions.

scConGraph requires python version 3.7+. Install directly from pip with:

pip install scConGraph

The LINE toolkit achieved in LINUX version should be downloaded and installed from https://github.com/tangjianpku/LINE.git before using scConGraph.

The vignette of scConGraph can be found in the project wiki.

The R scripts used for analyzing drug responses are located in the Analysis/Codes folder. The raw and intermediate data are stored in the Analysis/Data folder. Larger datasets are saved on the cloud.
If you have any questions about the codes, please contact the author.