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Since both Seurat and Scanpy are evolving rapidly, the safest way is to save your Seurat object into MatrixMarket format + metadata csv, and import them into Scanpy.


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If you launch like docker run -p 8888:8888 jupyter/r-notebook you will get the help page like a widget and a warning in your cell output. Check your browser, maybe is blocking pop-up elements.


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I think error is not related to ?. This is what I see when I try ?seq:


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Here is a code on github that can generate a csv file as well as a python dictionary. https://github.com/rahulnutron/scientific_name_to_common-name_converter


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I strongly suggest that you take your normalized counts, get the averages of different groups, and compare those ratios to the different designs. That said, you might not be able to replicate the fold changes from ~ genotype + time well in Excel. What that design does is basically say "Lots of the variance within each genotype/time point is due to the ...


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Set the column you don't want to NULL x$remove.column <- NULL


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Answer from @maximilian-press, converted from comment: Sometimes casting to as.numeric() will convert from two-dimensional matrix to one-dimensional vector. Based on the output you put into comments (which would be helpful in the question), I wonder if this has occurred and caused an issue. For data.matrix, I suggest reading docs for that function- it should ...


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Seurat does violin plots using ggplot, which orders based on the factor levels. You need to re-factor your grouping category so that the levels matches your preferred order: # default level sort order is alphabetical obj[["grouping"]] <- factor(unlist(obj[["grouping"]])) VlnPlot(obj, group.by = "grouping", features = c("...


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