SODB facilitates comprehensive exploration of spatial omics data

Z Yuan, W Pan, X Zhao, F Zhao, Z Xu, X Li, Y Zhao… - Nature …, 2023 - nature.com
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 …

Squidpy: a scalable framework for spatial omics analysis

G Palla, H Spitzer, M Klein, D Fischer, AC Schaar… - Nature …, 2022 - nature.com
Spatial omics data are advancing the study of tissue organization and cellular
communication at an unprecedented scale. Flexible tools are required to store, integrate and …

Enablers and challenges of spatial omics, a melting pot of technologies

T Alexandrov, J Saez‐Rodriguez… - Molecular Systems …, 2023 - embopress.org
Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of
publications presenting novel methods for obtaining spatially resolved information for any …

Aquila: a spatial omics database and analysis platform

Y Zheng, Y Chen, X Ding, KH Wong… - Nucleic Acids …, 2023 - academic.oup.com
Spatial omics is a rapidly evolving approach for exploring tissue microenvironment and
cellular networks by integrating spatial knowledge with transcript or protein expression …

Streamlining spatial omics data analysis with Pysodb

S Lin, F Zhao, Z Wu, J Yao, Y Zhao, Z Yuan - Nature Protocols, 2024 - nature.com
Advances in spatial omics technologies have improved the understanding of cellular
organization in tissues, leading to the generation of complex and heterogeneous data and …

Spatial omics technologies at multimodal and single cell/subcellular level

J Park, J Kim, T Lewy, CM Rice, O Elemento… - Genome Biology, 2022 - Springer
Spatial omics technologies enable a deeper understanding of cellular organizations and
interactions within a tissue of interest. These assays can identify specific compartments or …

SpatialData: an open and universal data framework for spatial omics

L Marconato, G Palla, KA Yamauchi, I Virshup… - Nature …, 2024 - nature.com
Spatially resolved omics technologies are transforming our understanding of biological
tissues. However, the handling of uni-and multimodal spatial omics datasets remains a …

In silico tissue generation and power analysis for spatial omics

EAG Baker, D Schapiro, B Dumitrascu, S Vickovic… - Nature …, 2023 - nature.com
As spatially resolved multiplex profiling of RNA and proteins becomes more prominent, it is
increasingly important to understand the statistical power available to test specific …

spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

B Pardo, A Spangler, LM Weber, SC Page, SC Hicks… - BMC genomics, 2022 - Springer
Background Spatially-resolved transcriptomics has now enabled the quantification of high-
throughput and transcriptome-wide gene expression in intact tissue while also retaining the …

SOTIP is a versatile method for microenvironment modeling with spatial omics data

Z Yuan, Y Li, M Shi, F Yang, J Gao, J Yao… - Nature …, 2022 - nature.com
The rapidly developing spatial omics generated datasets with diverse scales and modalities.
However, most existing methods focus on modeling dynamics of single cells while ignore …