Cannot find layers in this seurat object
WebJun 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. WebMar 23, 2024 · Seurat offers two workflows to identify molecular features that correlate with spatial location within a tissue. The first is to perform differential expression based on pre-annotated anatomical regions within the tissue, which may be determined either from unsupervised clustering or prior knowledge.
Cannot find layers in this seurat object
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WebThe 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. Weblabels. 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 points are being plotted. If using repel, set xnudge and ynudge to 0. xnudge, ynudge. Amount to nudge X and Y coordinates of ...
WebJun 25, 2024 · The text was updated successfully, but these errors were encountered: WebTo 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 …
WebFeb 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 … WebFeb 11, 2024 · object = P2dual, nn.name = "wknn", assay = "RNA", verbose = TRUE ) Warning: The following arguments are not used: reduction.model, return.model, n.neighbors, set.op.mix.ratio, …
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 …
WebMar 14, 2024 · When I create the Seurat object and load the metadata for it, all of the values in the nCount_RNA are decimal values instead of integers. How should I interpret this? Is there an issue with the data itself or something I can do to work around this? I ask because later on in my analysis, the functions can't seem to find the nCount_RNA object ... hanging belly supportWebMay 11, 2024 · Hi @skim245, as far as I know, you have to build the raw loom file from your bam file first, in order to be able to retrieve the spliced and unspliced reads.. Does this mean we have to create the loom file for the RNA velocity analysis and … hanging bench outdoorWebJun 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. hanging bench swing home depotWebJul 19, 2024 · Hello every one! I have 10X Genomics output from multiple runs. From each run, I created a Seurat Object from the output/filtered_gene_bc_matrices/ folders and then merged them into 1 seurat object.. I used the above merged object for all my clustering analysis and have exported this all as an RDS file. hanging bench swing outdoorWebOct 26, 2024 · You can extract the necessary values and add them directly the plot as a second layer using plot + geom_text().This is very similar to the inner workings of the … hanging betta fish bowlsWebNov 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 ... hanging bench pressWebJul 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). : hanging bench seat