Cannot find layers in this seurat object
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.
Cannot find layers in this seurat object
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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 ... 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.
WebJul 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. 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 …
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 ... 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 …
WebOct 10, 2024 · I created an integrated Seurat object by normalizing and running FindVariableFeatures() on 20 individual samples, then running FindIntegrationAnchors() and IntegrateData(). The integrated dataset is very large (over 100K cells). ... Cannot run PCA on integrated data #3589. Closed jgamache014 opened this issue Oct 10, 2024 · 10 …
WebDec 18, 2024 · Error: Cannot find 'umap' in this Seurat object. I have tried renaming and reinstalling umap-learn with reticulate::py_install(packages = 'umap-learn') however this isn't working, I am using python version 3.8, … dynatech systems ahmedabadWebJul 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). : dutch britton fire extinguishers annapolis mdWebOct 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 … dutch brickworkWebApr 30, 2024 · PadNames: Add names for unnamed or partially named objects; PB: Create a progress bar; RandomName: Generate a random string of characters; ReadH5: Load data from an HDF5 File; RegisterSCDisk: Get and Register 'scdisk' Subclasses; SaveH5Seurat: Save a 'Seurat' object to an h5Seurat file; SaveLoom: Save a 'Seurat' object to a loom file dynaware industrial incWebJun 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. dynatech suv bulletproofWebMar 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. dynaudio air control softwareWebSaving a dataset. Saving a Seurat object to an h5Seurat file is a fairly painless process. All assays, dimensional reductions, spatial images, and nearest-neighbor graphs are … dutch bridge holland