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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 …

Normally duplicated colnames are tolerated with matrices and sparse matrices, however, Seurat apparently does not do so, below is from the ? … ) For efficiency, Seurat uses sparse matrices so don't forget to convert your data matrices to sparse. …

You can use the group.by argument of the DimPlot() function. group.by accepts column names present in the meta.data column of the Seurat objects. …

That is because SCTransform (mostly) outputs discrete values, you can check the @slot of your Seurat object. …

Directly copy-pasting from one of the Seurat vignettes: # find markers for every cluster compared to all remaining cells, report only the positive ones pbmc.markers <- FindAllMarkers(pbmc, only.pos = TRUE …

marker would not mean much in terms of scRNA-seq, it might very well not be detected simply due to sensitivity ii) Use clustree do select the most plausible number of clusters (resolution parameter in Seurat … The package is compatible with Seurat and some other scRNA-seq packages. iii) Use silhouette width as a metric for clustering. …

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). rowSums …

It is absolutely necessary to remove low quality cells: In the case of CCA (and this applies to other "integration" or "data alignment" methods as well), one would need to use "anchors", basically sam …

Seurat has a nice CCA tutorial, you would not need the raw data, count data would be fine but you will need to be able to specify what data are coming from what source, the authors must have provided 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 …

variable.features.n sets the number of features (you can think of genes in the case of scRNA-seq) you would like to use for the downstream steps such as clustering. Basically, using a gene that is exp …

I believe the reason is simply LTA and LTB not being expressed (or their expression not being detected due to technical limitations). If you would set the pt.size argument to something else than 0, yo …

In your DoHeatmap() call, you do not provide features so the function does not know which genes/features to use for the heatmap. In your last function call, you are trying to group based on a continuo …

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.

In Seurat v3, there is a wide selection of different clustering algorithms but recommending one over the other would be beyond my expertise. … An alternative non-Seurat approach that aims to do the same is MNNCorrect from the scran package. …