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omnideconv / SimBu

Simulate pseudo-bulk RNAseq samples from scRNAseq expression data
http://omnideconv.org/SimBu/
GNU General Public License v3.0
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Example/tutorial operate/access output from simulate_bulk #42

Closed slieped closed 1 year ago

slieped commented 1 year ago

First, congratz for the excellent work and thanks for making it public!

Enhancement

Add an example on how to access the output data from the "simulate_bulk" function

Whereas in the example tutorial its super clear that the output its a SummarizedExperiment object, for more "noobie" users it might be good to show how to access to simulated pseudobulk from the output (i.e that the return is a list and should be accessed via outsimulation["bulk"])

Close and ignore this if you think its not needed at all. Again, thanks!

V

alex-d13 commented 1 year ago

Hi,

Thanks for the nice feedback. So you are talking about extending this section here: http://omnideconv.org/SimBu/articles/simulator_input_output.html#output, right?

Best, Alex

slieped commented 1 year ago

Exactly!

Or, at least, refer to that link after the simulate_bulk section (I am aware its mention in the create dataset section).

Again, great job with this tool!