Discover what's possible with spatial transcriptomics, including the additional depth it can add to single cell research projects, through these high-impact publications. Read now Human liver cancer; Visium Spatial Zhang S, et al. Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab...
(eggplant). The workshop introduced the participants to both theoretical concepts as well as hands-on tutorials for the analysis of spatial transcriptomics data. Publicly available data was available for this purpose, but users were welcome to analyze their own data in the context of the workshop...
Therefore, a broader view of gene behavior offers more accurate insights into cellular heterogeneity in single-cell or spatial transcriptomics data. Here, we describe SciGeneX (Single-cell informative Gene eXplorer), a R package implementing a neighborhood analysis and a graph partitioning method to ...
Spatial transcriptomics combines high-plex quantification with the spatial resolution of immunohistochemistry. This technology classifies tissue based on total mRNA within the morphological context of FFPE or frozen tissues. Spatial expression mapping is a powerful tool for examining cellular interactions, tiss...
SOAR: a spatial transcriptomics analysis resource to model spatial variability and cell type interactions. Preprint at bioRxiv https://doi.org/10.1101/2022.04.17.488596 (2022). Fan, Z., Chen, R. & Chen, X. SpatialDB: a database for spatially resolved transcriptomes. Nucleic Acids Res. https:...
今年3月 Nature子刊《Nature Methods》发表了一篇关于空间转录组学的全面综述:Museum of spatial transcriptomics,作者对1987年以来有关空间转录组学的文献进行了整理回顾,并对该领域的趋势进行了深入分析,如…
论文链接:Alignment and Integration of Spatial Transcriptomics Data Abstract 空间转录组学(ST)可测量组织切片中数千个点的 mRNA 表达,同时记录每个点的 2D 坐标。(Method)本文介绍了ST实验的概率对齐(PASTE)方法,从多个临近的组织切片中对齐和整合ST数据。(Detail)PASTE 使用最优传输公式计算一对切片的一致性,该公...
今年3月Nature子刊《Nature Methods》发表了一篇关于空间转录组学的全面综述:Museum of spatial transcriptomics,作者对1987年以来有关空间转录组学的文献进行了整理回顾,并对该领域的趋势进行了深入分析,如实验技术的使用、研究的物种/组织和使用的计算方法等。 技术背景-Prequel era 一些重要的空间转录组学技术可以追溯...
Spatial transcriptomics technologies developed in recent years can provide various information including tissue heterogeneity, which is fundamental in biological and medical research, and have been making significant breakthroughs. Single-cell RNA sequen
In this work, we present the InSTAnT toolkit to screen for subcellular colocalization patterns of RNA pairs and modules in an unbiased manner, through rigorous statistical analysis of single-molecule resolution spatial transcriptomics data. We define these patterns as new statistical phenomena that may...