Data Integration with LIGER

Joshua D. Welch



LIGER was initially introduced in Welch et al. 2019 as a method for integrating single-cell RNA-seq data across multiple technologies, species, and conditions. The method relies on integrative nonnegative matrix factorization (iNMF) to identify shared and dataset-specific factors.

LIGER can be used to compare and contrast experimental datasets in a variety of contexts, for instance:

Once multiple datasets are integrated, the package provides functionality for further data exploration, analysis, and visualization. Users can:


We have now made a documentation website for rliger 2.0.0. Please check it out for detailed introduction.

We have made a number of vignettes for typical types of analysis that can be performed with LIGER.

Meanwhile, since version 2.0.0, LIGER is massively updated for usability and interoperability with other packages. Below are links to the introduction of new features.