Integrating Single-Cell Profiles Across Modalities Using Manifold Alignment

To develop algorithms based on manifold alignment for integrating different types of single-cell measurements.

The Welch lab developed an open source R package, LIGER, for integrating multimodal datasets containing both trajectories and clusters. They released servel vignettes demonstrating how to use LIGER to integrate multiple single-cell RNA-seq datasets, jointly define cell types from single-cell RNA-seq and ATAC-seq, and jointly define cell types from single-cell RNA-seq and DNA methylation. They also developed a trajectory inference method that interfaces with LIGER, Topologizer.