WebMar 27, 2024 · The demultiplexing function HTODemux () implements the following procedure: We perform a k-medoid clustering on the normalized HTO values, which initially separates cells into K (# of samples)+1 clusters. We calculate a ‘negative’ distribution for HTO. For each HTO, we use the cluster with the lowest average value as the negative … WebJan 12, 2024 · After updating a Seurat version 2 object to a Seurat version 3 object using the UpdateSeuratObject function, I get the error: Error in [[.Seurat(object, …
Possible Subset Function Bug · Issue #2308 · satijalab/seurat
WebMar 23, 2024 · This tutorial demonstrates how to use Seurat (>=3.2) to analyze spatially-resolved RNA-seq data. While the analytical pipelines are similar to the Seurat workflow … WebJun 19, 2024 · The assays used by the pipelined R scripts have been modified as follows: (1) seurat_begin.py: if "log-normalization" is selected the saved object will have the … my free tips
Create an Assay object — CreateAssayObject • SeuratObject
Web# Set an Assay slot through the Seurat object count.data <-GetAssayData (object = pbmc_small [["RNA"]], slot = "counts") count.data <-as.matrix (x = count.data + 1) … WebJan 30, 2024 · I am try ing to estimate RNA velocity using Seurat. I have dropest file: counts.matrices.rds But I am getting error. My code is as follow. file<- readRDS(file … WebMay 14, 2024 · In your case, the prefix would be "RNA_snn_res.` (which would indicate that you clustered on the RNA assay using the SNN graph; the "0.5" bit indicates that you clustered at a resolution of 0.5). The seurat_clusters column is simply the latest clustering, and cannot be used in Clustree oft-1545