Cannot find layers in this seurat object

Author: pwza

August undefined, 2024

WebSaving 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 … 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, …

Cell Selector — CellSelector • Seurat - Satija Lab

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. 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 … inbox shows unread messages that aren\\u0027t there

Import gene list to Seurat to define cell types

WebMar 28, 2024 · Here, we describe important commands and functions to store, access, and process data using Seurat v5. To demonstrate commamnds, we use a dataset of 3,000 … WebMay 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 … 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 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) inbox simulations

r - Add Metadata to Seurat Object - Stack Overflow

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 … WebOct 27, 2024 · I am grateful if someone could help using csv file to load the UMAP/tSNE coordinate from Seurat object (rds file) to the anndata object (adata) in python. I used a stupid way but it worked: 1- save the rds file to loom file. 2- read the loom file: adataTemp = scv.read('seurat.loom') 3- put the umap back to adata: inbox setup in outlookWebJan 11, 2024 · 1. I am working with a R package called "Seurat" for single cell RNA-Seq analysis and I am trying to remove few genes in seuratobject (s4 class) from slot name … inclination\\u0027s ab

"WebApr 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 " - Cannot find layers in this seurat object

Cannot find layers in this seurat object

Saving and Loading Data from an h5Seurat File • …

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() ). 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 ...

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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:

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. 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 …

WebNov 9, 2024 · New issue No seurat_annotation in seurat Object for my data #5285 Closed Aya-Balbaa opened this issue on Nov 9, 2024 · 2 comments Aya-Balbaa on Nov 9, 2024 timoast completed on Nov 12, 2024 Sign up for free to join this conversation on GitHub . Already have an account? Sign in to comment WebNew data visualization methods in v3.0 - Satija Lab

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.

WebAn optional Seurat object; if passes, will return an object with the identities of selected cells set to ident. ident. An optional new identity class to assign the selected cells... Ignored. … inbox sign in hotmailWebOct 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 … inbox sitradWeblabels. 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 ... inclination\\u0027s adWebDefines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved … inbox sign upWebNov 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 … inclination\\u0027s aeWebJul 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. inclination\\u0027s akWebJun 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. inbox size