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Seurat objects have various slots where different types and forms of data are stored. For FateID you would need an expression matrix (with cells as columns and genes as rows) and this can be extracted …

The DimPlot() function of the new version of Seurat, Seurat v3 has a split.by argument, which splits the plot based on the levels of the variable provided. You basically need to provide a column from …

how to get this to arrange the UMAP plots into a 2x3 grid You can use the ncol parameter, which will set the number of columns in the "combined plot". And for future reference, if you get the help p …

Given the fact that you have RNA and ADT data (probably on the same set of cells), some colnames (which represent individual cells) would be duplicated. Normally duplicated colnames are tolerated with …

I wouldn't be surprised if the 15 cell types that you are expecting were mostly characterized via "protein-based" methods; antibody staining, flow cytometry using fluorophore coupled antibodies, ... T …

With a little bit of workaround: i) Add a new column to the data slot (only because your original subset() call does so but it can be raw counts or any other data matrix in your Seurat object). rowSu …

I believe it would be easier to answer the question by dividing it into related but more specific questions. Having said that, even if the answers below would be satisfactory, I would still post this …

If I understand your question correctly, you can simply use SetIdent() to change the "default identity" to your samples and then use FindMarker() with the ident.1 = "Double-KO" and ident.2 = "Shox2-KO …

You should have fed "1h" to your function call but you fed 1h instead. The latter is looking for an object with that name and as the error shows, there is no such object.

You have fed arguments to the MergeSeurat() function that it does not expect. In terms of objects, MergeSeurat() accepts only 2 arguments object1 and object2, please do ?MergeSeurat and see yourself. …

If the authors did not provide the raw counts, and I don't think it is compulsory, unfortunately you will need to download the raw data, align and count.

This seems to be an encoding problem (certain characters not being recognized), see this, this and also this. Probably the file "/cloud/project/SCG71.loom" is encoded with a format that is not include …

It looks like it is 10X data and I strongly suggest a dedicated single cell analysis package such as Seurat. You will most likely end up using one of these anyway for data analysis. Read10X() can be a …

Not a direct solution but some workarounds: As far as I know, Seurat can work with sparse matrices. The particular function of scran that you are using eats up quite some memory. I believe it is nee …

Your cluster labels come from graph clustering implemented in the FindClusters() function. The resulting clusters are then visualised with a 2D tSNE plot (via RunTSNE() and TSNEPlot()). So, your clust …