GTE quantifies batch effects for individual genes in single-cell data. If you have any suggestions or problems on this package, please contact Y. Zhou ([email protected]), or submit through this GitHub page directly.
To run GTE, install from GitHub through devtools directly:
install.packages('devtools')
library(devtools)
devtools::install_github("yzhou1999/GTE")Installation may take from a few seconds to a few minutes.
For usage examples, please see the vignettes directory of the repository.
We also provided several demo datasets, and our main program may take a few seconds to run on a standard laptop.
The codes and source data to benchmark the batch separation metrics please see here.
The datasets are available freely on public databases, and can also be downloaded in the Zenodo repository.
GTE has been successfully installed and used on Windows, Linux and Mac OS (R version >= 4.0.2).