Huidong Chen

SIMBA is a graph embedding method that jointly embeds single cells and their features into a common space, enabling diverse single-cell analysis tasks.

singlecellVR provides an accessible VR tool for visualizing single-cell data, supporting various modalities and offering a companion package for data conversion and pre-analyzed datasets.

The paper benchmarks 10 scATAC-seq analysis methods on synthetic and real datasets, finding SnapATAC, Cusanovich2018, and cisTopic perform best in separating cell populations across varying coverage and noise levels.

STREAM is an interactive pipeline for reconstructing and visualizing complex branching trajectories from single-cell transcriptomic and epigenomic data.