ZWang-Lab / G2S3

G2S3 (Sparse and Smooth Signal of Gene Graph-based imputation)

G2S3: a Sparse and Smooth Signal of Gene Graph-based imputation method for scRNA-seq data

G2S3 is an imputation method that applies graph signal processing to extract gene graph structure from scRNA-seq data and recover true expression levels by borrowing information from adjacent genes in the gene graph. It is computationally efficient for imputation in large-scale scRNA-seq datasets.

Installation Instructions:

Required software and packages

To use G2S3 in R, you will need to install both the R and Matlab toolboxes.

1. Matlab R2019b (https://au.mathworks.com)

2. R (http://www.r-project.org/)

3. UNLocBoX (https://epfl-lts2.github.io/unlocbox-html/)

4. GSPBOX (https://epfl-lts2.github.io/gspbox-html/download.html)

Install the required Matlab Toolboxes before running G2S3.m.

Usage instructions:

g2s3_config.R: R source code for configure running scripts for G2S3. It includes function to generate run_G2S3.m file in the folder which can be called in R.

example_script.R: an example to use G2S3 in R enviroment.

run_G2S3.m: example Matlab script to run G2S3.m.

example1.rds: example dataset.