stLearn: integrating spatial location, tissue morphology and gene expression to find cell types, cell-cell interactions and spatial trajectories within undissociated tissues

D Pham, X Tan, J Xu, LF Grice, PY Lam, A Raghubar… - BioRxiv, 2020 - biorxiv.org
Spatial Transcriptomics is an emerging technology that adds spatial dimensionality and
tissue morphology to the genome-wide transcriptional profile of cells in an undissociated …

Cell2location maps fine-grained cell types in spatial transcriptomics

V Kleshchevnikov, A Shmatko, E Dann… - Nature …, 2022 - nature.com
Spatial transcriptomic technologies promise to resolve cellular wiring diagrams of tissues in
health and disease, but comprehensive mapping of cell types in situ remains a challenge …

Projecting RNA measurements onto single cell atlases to extract cell type-specific expression profiles using scProjection

N Johansen, H Hu, G Quon - Nature Communications, 2023 - nature.com
Multi-modal single cell RNA assays capture RNA content as well as other data modalities,
such as spatial cell position or the electrophysiological properties of cells. Compared to …

Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES

MSB Raredon, J Yang, N Kothapalli, W Lewis… - …, 2023 - academic.oup.com
Motivation Recent years have seen the release of several toolsets that reveal cell–cell
interactions from single-cell data. However, all existing approaches leverage mean celltype …

Single-cell RNA-sequencing of the brain

R Cuevas-Diaz Duran, H Wei, JQ Wu - Clinical and translational medicine, 2017 - Springer
Single-cell RNA-sequencing (scRNA-seq) is revolutionizing our understanding of the
genomic, transcriptomic and epigenomic landscapes of cells within organs. The mammalian …

[PDF][PDF] SnapShot: spatial transcriptomics

L Larsson, L Bergenstråhle, M He, Z Andrusivova… - Cell, 2022 - cell.com
Spatially resolved transcriptomics methodologies using RNA sequencing principles have
and will continue to contribute to decode the molecular landscape of tissues. Linking …

Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists

X Zhu, TK Wolfgruber, A Tasato, C Arisdakessian… - Genome medicine, 2017 - Springer
Background Single-cell RNA sequencing (scRNA-Seq) is an increasingly popular platform
to study heterogeneity at the single-cell level. Computational methods to process scRNA …

SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution

A Sountoulidis, A Liontos, HP Nguyen, AB Firsova… - PLoS …, 2020 - journals.plos.org
Changes in cell identities and positions underlie tissue development and disease
progression. Although single-cell mRNA sequencing (scRNA-Seq) methods rapidly …

Profiling of single‐cell transcriptomes

W Chen, V Gardeux, A Meireles‐Filho… - Current protocols in …, 2017 - Wiley Online Library
Complex biological systems are composed of multiple cell types whose transcriptional
activity can vary due to differences in cell state, environmental stimulation, or intrinsic …

NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport

N Moriel, E Senel, N Friedman, N Rajewsky… - Nature protocols, 2021 - nature.com
Single-cell RNA-sequencing (scRNA-seq) technologies have revolutionized modern
biomedical sciences. A fundamental challenge is to incorporate spatial information to study …