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Review
Biochemistry & Molecular Biology
Kyongho Choe et al.
Summary: Development from single cells to multicellular tissues and organs involves differentiation, which is not merely the replication of cells. Previous research has focused on differences in gene expression profiles, but has been limited in understanding the molecular mechanisms of differentiation. Advancements in genomics, particularly single-cell RNA-sequencing (scRNA-seq), have enabled a better understanding of differentiation and cell lineage. However, the loss of spatial information during scRNA-seq has led to the emergence of spatial transcriptomics as a discipline and the development of tools to address this limitation.
Article
Biochemical Research Methods
Giovanni Palla et al.
Summary: Squidpy is a Python framework that combines tools from omics and image analysis to efficiently store, manipulate, and visualize spatial omics data. It is extensible and can be interfaced with other libraries for scalable analysis of spatial omics data.
Editorial Material
Oncology
Ana C. Anderson et al.
Editorial Material
Biochemical Research Methods
Jennie L. Close et al.
Summary: Spatially resolved transcriptomics has great potential in unraveling the organization of brain cell types and their relationship with connectivity, circuit dynamics, behavior, and disease, but technical challenges need to be overcome to fully realize its potentials.
Editorial Material
Biochemical Research Methods
Vivien Marx
Summary: Nature Methods has named spatially resolved transcriptomics as Method of the Year 2020.
Article
Biotechnology & Applied Microbiology
Ruben Dries et al.
Summary: Giotto is a comprehensive open-source toolbox for spatial data analysis and visualization, providing end-to-end analysis with a wide range of algorithms for characterizing tissue composition and cellular interactions, as well as integrating single-cell RNAseq data for cell-type enrichment analysis. The visualization module allows interactive visualization of analysis outputs and imaging features, demonstrating its general applicability across diverse datasets and platforms.
Article
Multidisciplinary Sciences
Mahmoud Ghandi et al.
Article
Biochemical Research Methods
Valentine Svensson et al.
Article
Biotechnology & Applied Microbiology
F. Alexander Wolf et al.
Article
Immunology
Gabriela Bindea et al.
Article
Biochemical Research Methods
Peter Langfelder et al.
BMC BIOINFORMATICS
(2008)