Benchmarking and integration of methods for deconvoluting spatial transcriptomic data

L Yan, X Sun - Bioinformatics, 2023 - academic.oup.com
Motivation The rapid development of spatial transcriptomics (ST) approaches has provided
new insights into understanding tissue architecture and function. However, the gene …

EnDecon: cell type deconvolution of spatially resolved transcriptomics data via ensemble learning

JJ Tu, HS Li, H Yan, XF Zhang - Bioinformatics, 2023 - academic.oup.com
Motivation Spatially resolved gene expression profiles are the key to exploring the cell type
spatial distributions and understanding the architecture of tissues. Many spatially resolved …

A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics

H Li, J Zhou, Z Li, S Chen, X Liao, B Zhang… - Nature …, 2023 - nature.com
Spatial transcriptomics technologies are used to profile transcriptomes while preserving
spatial information, which enables high-resolution characterization of transcriptional patterns …

Spotless, a reproducible pipeline for benchmarking cell type deconvolution in spatial transcriptomics

C Sang-Aram, R Browaeys, R Seurinck, Y Saeys - Elife, 2024 - elifesciences.org
Spatial transcriptomics (ST) technologies allow the profiling of the transcriptome of cells
while keeping their spatial context. Since most commercial untargeted ST technologies do …

SD2: spatially resolved transcriptomics deconvolution through integration of dropout and spatial information

H Li, H Li, J Zhou, X Gao - Bioinformatics, 2022 - academic.oup.com
Motivation Unveiling the heterogeneity in the tissues is crucial to explore cell–cell
interactions and cellular targets of human diseases. Spatial transcriptomics (ST) supplies …

SpatialDWLS: accurate deconvolution of spatial transcriptomic data

R Dong, GC Yuan - Genome biology, 2021 - Springer
Recent development of spatial transcriptomic technologies has made it possible to
characterize cellular heterogeneity with spatial information. However, the technology often …

A comprehensive comparison on cell-type composition inference for spatial transcriptomics data

J Chen, W Liu, T Luo, Z Yu, M Jiang… - Briefings in …, 2022 - academic.oup.com
Spatial transcriptomics (ST) technologies allow researchers to examine transcriptional
profiles along with maintained positional information. Such spatially resolved transcriptional …

SpaDecon: cell-type deconvolution in spatial transcriptomics with semi-supervised learning

K Coleman, J Hu, A Schroeder, EB Lee, M Li - Communications Biology, 2023 - nature.com
Spatially resolved transcriptomics (SRT) has advanced our understanding of the spatial
patterns of gene expression, but the lack of single-cell resolution in spatial barcoding-based …

Spatially informed cell-type deconvolution for spatial transcriptomics

Y Ma, X Zhou - Nature biotechnology, 2022 - nature.com
Many spatially resolved transcriptomic technologies do not have single-cell resolution but
measure the average gene expression for each spot from a mixture of cells of potentially …

Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution

B Li, W Zhang, C Guo, H Xu, L Li, M Fang, Y Hu… - Nature …, 2022 - nature.com
Spatial transcriptomics approaches have substantially advanced our capacity to detect the
spatial distribution of RNA transcripts in tissues, yet it remains challenging to characterize …