Unsupervised spatially embedded deep representation of spatial transcriptomics

Abstract Optimal integration of transcriptomics data and associated spatial information is essential towards fully exploiting spatial transcriptomics to dissect tissue heterogeneity and map out inter-cellular communications. We present SEDR, which uses a deep autoencoder coupled with a masked self-s...

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Bibliographic Details

Published in:	Genome Medicine
Main Authors:	Hang Xu, Huazhu Fu, Yahui Long, Kok Siong Ang, Raman Sethi, Kelvin Chong, Mengwei Li, Rom Uddamvathanak, Hong Kai Lee, Jingjing Ling, Ao Chen, Ling Shao, Longqi Liu, Jinmiao Chen
Format:	Article
Language:	English
Published:	BMC 2024-01-01
Subjects:	Spatial transcriptomics Spatial clustering Variational graph auto-encoder Batch integration Trajectory inference Gene imputation
Online Access:	https://doi.org/10.1186/s13073-024-01283-x