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LIGER (Linked Inference of Genomic Experimental Relationships)

Now we have a comprehensive documentation site for the latest version of rliger (2.0)!

LIGER (installed as rliger ) is a package for integrating and analyzing multiple single-cell datasets, developed by the Macosko lab and maintained/extended by the Welch lab. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors.

Check out our Cell paper for a more complete description of the methods and analyses. To access data used in our SN and BNST analyses, visit our study “SCP466” on the Single Cell Portal.

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 also designed LIGER to interface with existing single-cell analysis packages, including Seurat.


If you use LIGER in your research please cite our paper correspondingly:

Joshua D. Welch and et al., Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity, Cell, VOLUME 177, ISSUE 7, P1873-1887.E17 (2019), https://doi.org/10.1016/j.cell.2019.05.006

Liu, J., Gao, C., Sodicoff, J. et al. Jointly defining cell types from multiple single-cell datasets using LIGER. Nat Protoc 15, 3632–3662 (2020), https://doi.org/10.1038/s41596-020-0391-8

Gao, C., Liu, J., Kriebel, A.R. et al. Iterative single-cell multi-omic integration using online learning. Nat Biotechnol 39, 1000–1007 (2021), https://doi.org/10.1038/s41587-021-00867-x

Kriebel, A.R., Welch, J.D. UINMF performs mosaic integration of single-cell multi-omic datasets using nonnegative matrix factorization. Nat Commun 13, 780 (2022), https://doi.org/10.1038/s41467-022-28431-4


If you have any questions, comments, or suggestions, you are welcomed to open an Issue!


For usage examples and guided walkthroughs, check the vignettes directory of the repo.

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.

If you need to refer to the tutorials for the old version of rliger, please check the GitHub archive v1.0.1, download the desired rendered HTML files and open them in your browser.

Sample Datasets

The rliger package provides different types of small toy dataset for basic demos of the functions. After attaching the package in an R session, you can load them with:


We also provide a set of datasets for real-world style demos, including scRNAseq, scATACseq, spatial transcriptomics and DNA methylation data. They are described in detail in the articles that make use of them. Please check them out from the links above.