SPANN: annotating single-cell resolution spatial transcriptome data with scRNA-seq data

M Yuan, H Wan, Z Wang, Q Guo… - Briefings in …, 2024 - academic.oup.com
Motivation The rapid development of spatial transcriptome technologies has enabled
researchers to acquire single-cell-level spatial data at an affordable price. However …

stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics

C Shengquan, Z Boheng, C Xiaoyang… - …, 2021 - academic.oup.com
Motivation Single-cell RNA sequencing (scRNA-seq) techniques have revolutionized the
investigation of transcriptomic landscape in individual cells. Recent advancements in spatial …

scMAGS: Marker gene selection from scRNA-seq data for spatial transcriptomics studies

Y Baran, B Doğan - Computers in Biology and Medicine, 2023 - Elsevier
Abstract Single-Cell RNA sequencing (scRNA-seq) has provided unprecedented
opportunities for exploring gene expression and thus uncovering regulatory relationships …

STellaris: a web server for accurate spatial mapping of single cells based on spatial transcriptomics data

X Li, C Xiao, J Qi, W Xue, X Xu, Z Mu… - Nucleic acids …, 2023 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) provides insights into gene expression
heterogeneities in diverse cell types underlying homeostasis, development and pathological …

webSCST: an interactive web application for single-cell RNA-sequencing data and spatial transcriptomic data integration

Z Zhang, F Cui, W Su, L Dou, A Xu, C Cao… - Bioinformatics, 2022 - academic.oup.com
Integrative analysis of single-cell RNA-sequencing (scRNA-seq) data with spatial data for
the same species and organ would provide each cell sample with a predictive spatial …

SpaGE: spatial gene enhancement using scRNA-seq

T Abdelaal, S Mourragui, A Mahfouz… - Nucleic acids …, 2020 - academic.oup.com
Single-cell technologies are emerging fast due to their ability to unravel the heterogeneity of
biological systems. While scRNA-seq is a powerful tool that measures whole-transcriptome …

Probabilistic cell/domain-type assignment of spatial transcriptomics data with SpatialAnno

X Shi, Y Yang, X Ma, Y Zhou, Z Guo… - Nucleic Acids …, 2023 - academic.oup.com
In the analysis of both single-cell RNA sequencing (scRNA-seq) and spatially resolved
transcriptomics (SRT) data, classifying cells/spots into cell/domain types is an essential …

Accurate and Flexible Single Cell to Spatial Transcriptome Mapping with Celloc

W Yin, X Wu, L Chen, Y Wan, Y Zhou - Small Science, 2024 - Wiley Online Library
Accurate mapping between single‐cell RNA sequencing (scRNA‐seq) and low‐resolution
spatial transcriptomics (ST) data compensates for both limited resolution of ST data and …

spSeudoMap: cell type mapping of spatial transcriptomics using unmatched single-cell RNA-seq data

S Bae, H Choi, DS Lee - Genome Medicine, 2023 - Springer
Since many single-cell RNA-seq (scRNA-seq) data are obtained after cell sorting, such as
when investigating immune cells, tracking cellular landscape by integrating single-cell data …

Adjustment of scRNA-seq data to improve cell-type decomposition of spatial transcriptomics

L Wang, Y Hu, L Gao - Briefings in Bioinformatics, 2024 - academic.oup.com
Most sequencing-based spatial transcriptomics (ST) technologies do not achieve single-cell
resolution where each captured location (spot) may contain a mixture of cells from …