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) WebNew data visualization methods in v3.0 - Satija Lab
Adding metadata to Seurat object - Bioinformatics Stack …
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 … 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 tips for fighting the flu
Import gene list to Seurat to define cell types
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 ... 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 ... 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 … tips for fighting jevil