Group Technical Effects

Implementation of the GTE (Group Technical Effects) model for single-cell data. GTE is a quantitative metric to assess batch effects for individual genes in single-cell data. For a single-cell dataset, the user can calculate the GTE value for individual features (such as genes), and then identify the highly batch-sensitive features. Removing these highly batch-sensitive features results in datasets with low batch effects.

GTEs R package

GTE model quantifies batch effects for individual genes in single-cell data.

Installation

To run GTEs package, install from GitHub through devtools directly:

install.packages('devtools')
library(devtools)
devtools::install_github("yzhou1999/GTEs")

Usage

See below for usage examples.

• Group technical effects calculation and highly batch-sensitive genes (HBGs) selection

Dependencies

GTEs has been successfully installed and used on Windows, Linux and Mac OS (R version >= 4.0.2).