RT Journal Article
SR Electronic
T1 Latent periodic process inference from single-cell RNA-seq data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 625566
DO 10.1101/625566
A1 Shaoheng Liang
A1 Fang Wang
A1 Jincheng Han
A1 Ken Chen
YR 2019
UL http://biorxiv.org/content/early/2019/05/02/625566.abstract
AB Convoluted biological processes underlie the development of multicellular organisms and diseases. Advances in scRNA-seq make it possible to study these processes from cells at various developmental stages. Achieving accurate characterization is challenging, however, particularly for periodic processes, such as cell cycles. To address this, we developed Cyclum, a novel AutoEncoder approach that characterizes circular trajectories in the high-dimensional gene expression space. Cyclum substantially improves the accuracy and robustness of cell-cycle characterization beyond existing approaches. Applying Cyclum to removing cell-cycle effects leads to substantially improved delineations of cell subpopulations, which is useful for establishing various cell atlases and studying tumor heterogeneity. Cyclum is available at https://github.com/KChen-lab/cyclum.