[HTML][HTML] Statistical and machine learning methods for spatially resolved transcriptomics with histology
Recent developments in spatially resolved transcriptomics (SRT) technologies have
enabled scientists to get an integrated understanding of cells in their morphological context …
enabled scientists to get an integrated understanding of cells in their morphological context …
ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data
V Gardeux, FPA David, A Shajkofci, PC Schwalie… - …, 2017 - academic.oup.com
Motivation Single-cell RNA-sequencing (scRNA-seq) allows whole transcriptome profiling of
thousands of individual cells, enabling the molecular exploration of tissues at the cellular …
thousands of individual cells, enabling the molecular exploration of tissues at the cellular …
Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data
Single-cell RNA-sequencing (scRNAseq) technologies are rapidly evolving. Although very
informative, in standard scRNAseq experiments, the spatial organization of the cells in the …
informative, in standard scRNAseq experiments, the spatial organization of the cells in the …
Splotch: robust estimation of aligned spatial temporal gene expression data
Spatial genomics technologies enable new approaches to study how cells interact and
function in intact multicellular environments but present a host of technical and …
function in intact multicellular environments but present a host of technical and …
SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes
Spatially resolved gene expression profiles are key to understand tissue organization and
function. However, spatial transcriptomics (ST) profiling techniques lack single-cell …
function. However, spatial transcriptomics (ST) profiling techniques lack single-cell …
ST Pipeline: an automated pipeline for spatial mapping of unique transcripts
Motivation In recent years we have witnessed an increase in novel RNA-seq based
techniques for transcriptomics analysis. Spatial transcriptomics is a novel RNA-seq based …
techniques for transcriptomics analysis. Spatial transcriptomics is a novel RNA-seq based …
STOmicsDB: a database of spatial transcriptomic data
Recent technological development in spatial transcriptomics allows researchers to measure
gene expression of cells and their spatial locations at the almost single-cell level, which …
gene expression of cells and their spatial locations at the almost single-cell level, which …
Spatial mapping of cell types by integration of transcriptomics data
A Andersson, J Bergenstråhle, M Asp, L Bergenstråhle… - bioRxiv, 2019 - biorxiv.org
Spatial transcriptomics and single cell RNA-sequencing offer complementary insights into
the transcriptional expression landscape. We here present a probabilistic method that …
the transcriptional expression landscape. We here present a probabilistic method that …
Identifying spatial co-occurrence in healthy and inflamed tissues (ISCHIA)
Sequencing-based spatial transcriptomics (ST) methods allow unbiased capturing of RNA
molecules at barcoded spots, charting the distribution and localization of cell types and …
molecules at barcoded spots, charting the distribution and localization of cell types and …
Reconstruction of the cell pseudo-space from single-cell RNA sequencing data with scSpace
Tissues are highly complicated with spatial heterogeneity in gene expression. However, the
cutting-edge single-cell RNA-seq technology eliminates the spatial information of individual …
cutting-edge single-cell RNA-seq technology eliminates the spatial information of individual …