Create seurat spatial object. project Mar 20, 2026 · Spatial Object Cl...
Create seurat spatial object. project Mar 20, 2026 · Spatial Object Classes Spatial information is stored in the images slot of the Seurat object. Description Wrapper to transform existing Seurat object into an SpaCoObject. Kapourani@ed. Kapourani C. While the analytical pipelines are similar to the Seurat workflow for single-cell RNA-seq analysis, we introduce updated interaction and visualization tools, with a particular emphasis on the integration of spatial and molecular information. R Create a new CellChat object from a data matrix, Seurat or SingleCellExperiment object Description Create a new CellChat object from a data matrix, Seurat or SingleCellExperiment object Usage. There is a wealth of software that utilizes single-cell RNA-seq (scRNA-seq) data to deconvolve spatial transcriptomic spots, which currently are not yet at single-cell resolution. frame with spatially-resolved molecule information or a Molecules object assay Name of associated assay key Key for these spatial coordinates misc A list of miscellaneous information to store with the object name When coords is a data. 2) to analyze spatially-resolved RNA-seq data. In this vignette, we present an introductory workflow for creating a multimodal Seurat object and performing an initial analysis. Should be a data. For example, we demonstrate how to cluster a CITE-seq dataset on the basis of the measured cellular transcriptomes, and subsequently discover cell surface proteins that are enriched in each cluster. frame, specify if Nov 10, 2023 · In sqjin/CellChat: Inference and analysis of cell-cell communication from single-cell and spatial transcriptomics data View source: R/CellChat_class. Jun 17, 2025 · Overview This tutorial demonstrates how to use Seurat (>=3. A. data") Arguments Value Returns a SpaCoObject with all slots filled necessary to perform the spatial component analysis. We have previously introduced a spatial framework which is compatible with sequencing-based technologies, like the 10x Genomics Visium system, or SLIDE-seq. If a single sample, returns a Seurat object. After a couple hours, I encountered this error. ac. Row names in the metadata need to match the column names of the counts matrix. uk Hi, I'm trying to integrate 17 Seurat objects on RStudio. Is t Additional cell-level metadata to add to the Seurat object. Wrapper to transform existing Seurat object into an SpaCoObject. Bioconductor has a spatial experiment object which is extended from the SingleCellExperiment object. This tutorial will cover the following tasks Nov 22, 2022 · Value List of Seurat objects equal the number of samples in the sample metadata file. Aug 20, 2025 · Overview In this vignette, we introduce a Seurat extension to analyze new types of spatially-resolved data. Oct 12, 2020 · Hi, I was wondering if you have advice on how to create a spatial Seurat object without using the SpaceRanger output data - for example, from published data using the pre-Visium ST technology. frame where the rows are cell names and the columns are additional metadata fields. Mar 30, 2023 · Seurat nicely integrated the spatial information to the Seurat object, so we can plot conveniently. Here we provide protocols for implementing Seurat and Giotto packages to elucidate cell-type distribution in our example human ureter scRNA-seq dataset. We also describe how to create a stand-alone interactive web Arguments passed to other methods molecules A data. Depending on the technology, different S3 classes are used to manage coordinates and images. Usage seurat_to_spaco(SeuratObject, assay = "SCT", n_image = 1, layer = "scale. Class Hierarchy and Methods All spatial classes implement a common set of generics to allow the Seurat plotting engine to interact with them regardless of the underlying technology. Author (s) C. frame, Centroids, or Segmentation, name to store coordinates as type When providing a data. zevys mgiiw qdllksu kvnd vodyeso
