WebDec 10, 2024 · > so.RunPrestoAll <- RunPrestoAll(object = SmallRO, assay = "RNA") Calculating cluster 0 Calculating cluster 1 ... etc Calculating cluster 12 Warning: No DE genes identified Warning: The following tests were not performed: Warning: When testing 0 versus all: Please only specify either assay or reduction. ... etc Warning: When testing … WebFeb 17, 2024 · Hi, Thank you for your reply Josephine! I have updated our documentation to add how to use the information stored in a Seurat object with version 3.0+ as we only had that for older versions. If you only intend to use this matrix for infercnv, you are not required to use the "as.matrix()" call since infercnv allows sparse matrices (the format which …
Assay · satijalab/seurat Wiki · GitHub
WebMay 27, 2024 · To use this file with Seurat and SeuratDisk, you'll need to read it in Python and save it out using the gzip compression import anndata adata = anndata . read ( … WebApr 11, 2024 · Seurat object was first converted to the CDS object, and then the significantly changed genes were identified using the differential GeneTest function to evaluate the differential state of the cells. sharon elder
Add scGSEA to Seurat Wrappers by melania15 · Pull Request #147 ...
WebMar 27, 2024 · Multi-Assay Features. With Seurat, you can easily switch between different assays at the single cell level (such as ADT counts from CITE-seq, or integrated/batch-corrected data). Most functions now take an assay parameter, but you can set a Default Assay to avoid repetitive statements. 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 … 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) … sharone jersey advantage mortgage