I was able to concatenate my loom objects into 1 object and converted it to Seurat object, but this object has not been in anyway processed (e.g., normalise etc that are typically done in scVelo pipeline). How might I add the ambiguous, matrix, spliced, unspliced to my Seurat GEX clus...
I want to extract expression matrix in different stages (after removing constant features, removing the cell cycle effect, etc.) from Seurat object. Is there any command to do it easily? Thanks Jared. You could use either data slot, or scale.data slot after SCTransform. ...
R does not display output Error in the predict function RStudio breaks on FreeBSD: "TypeError: undefined is not an object (evaluating 'window.desktopHooks.notifyRCrashed')" How to use crawler with Rcrawler for automatic download in r? Relabel and merge the fasta files How to deal...
Hi all, I would like to try another package for differential expression analysis, once after having my SeuratObject filtered, normalized and aligned following instructions for integrated analysis. How can I extract only counts with cell ...
Hello. Is it possible to add new metadata to categorize a group of samples? I usually use AddMetaData() to add sample identities or groupings to each of the samples/seurat objects, but I don't know how to do it in an integrated object. I previously integrated samples 1-10 and already...
Hey, I am currently working with a SeuratObject from one of our collaborators. This Object is a merged SeuratObject from seven different replicates. I want to unmerge/split the Object into each replicate so I can cluster them together in...