Webcolnames (seurat_object) provides a vector of cell names in a given Seurat object. Here whatever cell that is in the All_Samples_GeneA_Pos object would be GeneA_Pos and whatever is not GeneB_Pos. To better control the behavior, you can use a "nested" ifelse (); you can have another ifelse () instead of the "GeneB_Pos" bit above. WebDec 7, 2024 · library ( Signac) library ( Seurat) library ( GenomeInfoDb) library (EnsDb.Hsapiens.v75) library ( ggplot2) library ( patchwork) set.seed (1234) Pre-processing workflow When pre-processing chromatin data, Signac uses information from two related input files, both of which can be created using CellRanger: Peak/Cell matrix.
Get, set, and manipulate an object
WebFeb 4, 2024 · # change ident back to Donor data <- SetAllIdent(object = data, id = "Donor") OBS! Each time you want to change colors in a gene plot, you need to change the identity class value in the seurat object in the slot data@ident. Perhaps there is a better way, but I did not find a solution. WebJul 9, 2024 · Solution 2. I tried several R packages (mygene, org.Hs.eg.db, biomaRt, EnsDb.Hsapiens.v79) to convert Ensembl.gene to gene.symbol, and found that the EnsDb.Hsapiens.v79 package / gene database provides the best conversion quality (in terms of being able to convert most of Ensembl.gene to gene.symbol). Install the … gogear cozy buds review
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WebJul 26, 2024 · I'm using Seurat to analyze single cell RNA sequencing data and I'm attempting to rename genes/features from the chick to that of the zebrafish. I've used … WebJun 17, 2024 · How I know Seurat uses which gene name please This is my list CD45 MHC II CD11b Ly6C Ly6G F4/80 CD11c CD38 Arg1 SiglecF CD206 CD62L CD103 iNOS PD-L1 TNFa CD64 TCRgd Foxp3 RORgt CD8α Tbet CD25 IFN-γ CD44 CD86 CD80 PD-1 B220 NK1.1 CD19 CD4 TCR β From this list only 6 genes being mapped on the Seurat data … WebFeb 15, 2024 · 1 Answer Sorted by: 0 You have the arguments mixed up. Your keytype is SYMBOL and what you need is ncbi-geneid s (aka ENTREZID (old name)) mapIds (org.Hs.eg.db, keys = genelist$Name, column = "ENTREZID", keytype = … gogear automotive tower fan review