Cannot find layers in this seurat object
WebMar 3, 2024 · Hi, Please run RunPCA() before you do RPCA based integration. Please set your DefaultAssay to the correct assay (the assay you run your RunPCA() ). WebNov 14, 2024 · I am trying to add labels to my data and I am running into issues. I am trying to set up all the metadata in an Excel sheet and import that into Seurat. I am looking to add labels like patient ID, HPV Status etc. Here is what I have tried so far: • Once I import my data and create a Seurat object, I exported the [email protected] table.
Cannot find layers in this seurat object
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WebJun 19, 2024 · Maybe you can try Seurat::AddModuleScore (), then FeaturePlot () and see if some of your B cells are different. After plotting this on GenePlot (), perhaps you can set a cutoff, then assign identities. Alternatively, use your B cell gene list in RunPCA (object, pc.genes = yourgenelist) instead of the usual variable genes. WebNew data visualization methods in v3.0 - Satija Lab
WebAug 16, 2024 · Help with error: Cannot find 'Group' in this Seurat object #4 Open sjspielman opened this issue on Aug 16, 2024 · 4 comments on Aug 16, 2024 Sign up for free to join this conversation on GitHub . Already have an account? Sign in to comment Assignees No one assigned Labels None yet Projects None yet Milestone No milestone … WebNov 19, 2024 · plot. A ggplot2 plot with a GeomPoint layer. points. A vector of points to label; if NULL, will use all points in the plot. labels. A vector of labels for the points; if NULL, will use rownames of the data provided to the plot at the points selected. repel. Use geom_text_repel to create a nicely-repelled labels; this is slow when a lot of ...
WebJul 2, 2024 · NA in the sparseMatrix after using log normalization. Then when I used , it created a lot of zeros. I guess when feeded this scaled data to , removed columns/rows having variance = 0 and the final matrix was smaller than their expected number of left/right singular vectors. Fyi, this is my data (a Seurat object). : WebJun 25, 2024 · The text was updated successfully, but these errors were encountered:
WebThe loom method for as.Seurat will try to automatically fill in a Seurat object based on data presence. For example, if no normalized data is present, then scaled data, dimensional …
WebJul 7, 2024 · 1. I have a Seurat object of 8 patients. I want to add metadata to that so that I have origin of each cell. At the moment UMAP just shows a bunch of cells while I want to … how to smoke a 20 pound brisketWebDefines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved … novant health mt islandWebThe concept of global objects in Seurat is designed as an extension to the assay-centric nature of objects. In Seurat, each assay is considered to be one experiment or measurement of data for a common group of cells. These assays are then used to generate working summaries, such as reduced dimension space or nearest-neighbor graphs. novant health multiple sclerosis careWebTo add the metadata i used the following commands. First I extracted the cell names from the Seurat object. > Cells <- WhichCells (seurat_object) Then I created a list of the morphologically determined cell types using numbers 1-3 this NOTE: the list is much longer but abbreviated as the first 3 here. > MorphCellTypes = c (1,2,3) how to smoke a 16 lb beef brisketWebFeb 25, 2024 · To remove an Assay from a Seurat object, please set the assay as NULL using the double bracket [[setter (eg.ch.integrated[['integrated']] <- NULL). We strongly urge users to not rely on calling slots directly using @, as this doesn't take care of all references to the underlying data.For more details about the getters and setters, please see our … how to smoke a 6 pound brisketWebNov 10, 2024 · Error: Cannot find 'map' in this Seurat object Execution halted The text was updated successfully, but these errors were encountered: All reactions. Copy link Collaborator. yuhanH commented … how to smoke a 6lb brisketWebJun 13, 2024 · Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. how to smoke a 6 lb pork loin