[HTML][HTML] Best practices for single-cell analysis across modalities
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …
[HTML][HTML] An introduction to spatial transcriptomics for biomedical research
CG Williams, HJ Lee, T Asatsuma, R Vento-Tormo… - Genome Medicine, 2022 - Springer
Single-cell transcriptomics (scRNA-seq) has become essential for biomedical research over
the past decade, particularly in developmental biology, cancer, immunology, and …
the past decade, particularly in developmental biology, cancer, immunology, and …
[HTML][HTML] High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis
A Janesick, R Shelansky, AD Gottscho… - Nature …, 2023 - nature.com
Single-cell and spatial technologies that profile gene expression across a whole tissue are
revolutionizing the resolution of molecular states in clinical samples. Current commercially …
revolutionizing the resolution of molecular states in clinical samples. Current commercially …
[HTML][HTML] Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST
Spatial transcriptomics technologies generate gene expression profiles with spatial context,
requiring spatially informed analysis tools for three key tasks, spatial clustering, multisample …
requiring spatially informed analysis tools for three key tasks, spatial clustering, multisample …
[HTML][HTML] A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics
Spatial transcriptomics technologies are used to profile transcriptomes while preserving
spatial information, which enables high-resolution characterization of transcriptional patterns …
spatial information, which enables high-resolution characterization of transcriptional patterns …
The scverse project provides a computational ecosystem for single-cell omics data analysis
Single-cell omics technologies have enabled the creation of comprehensive cell atlases
across tissues and species and delivered key insights into the biological mechanisms …
across tissues and species and delivered key insights into the biological mechanisms …
[HTML][HTML] Spatially resolved multiomics of human cardiac niches
The function of a cell is defined by its intrinsic characteristics and its niche: the tissue
microenvironment in which it dwells. Here we combine single-cell and spatial …
microenvironment in which it dwells. Here we combine single-cell and spatial …
SODB facilitates comprehensive exploration of spatial omics data
Spatial omics technologies generate wealthy but highly complex datasets. Here we present
Spatial Omics DataBase (SODB), a web-based platform providing both rich data resources …
Spatial Omics DataBase (SODB), a web-based platform providing both rich data resources …
[HTML][HTML] An integrated single cell and spatial transcriptomic map of human white adipose tissue
To date, single-cell studies of human white adipose tissue (WAT) have been based on small
cohort sizes and no cellular consensus nomenclature exists. Herein, we performed a …
cohort sizes and no cellular consensus nomenclature exists. Herein, we performed a …
scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics
We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial
omics data, including various cell states, experimental designs and feature modalities, by …
omics data, including various cell states, experimental designs and feature modalities, by …