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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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Cannot find CreateBigSingleRObject function #56

Open tkapello opened 5 years ago

tkapello commented 5 years ago

Hi,

I am new to SingleR and I wanted to apply a dataset with ~50,000 cells. I looked for the CreateBigSingleRObject function as per the tutorial, but it did not appear. I have installed SingleR 0.2.2. to my computer, could this be a version issue?

Thanks, Theo

dviraran commented 5 years ago

Hi,

Very weird, this is the only master version. Are you sure the library is loaded correctly? maybe the installation didn't go through?

Best, Dvir

tkapello commented 5 years ago

I re-installed SingleR c. 0.2.2 and now it is there. May I also ask whether the standard downstream pipeline described in the SingleR tutorial can be applied in big dataset analysis, e.g. SingleR.PlotTsne(), SingleR.DrawHeatmap() for visualising the tSNE plots and heatmaps of these big datasets?

dviraran commented 5 years ago

If the CreateBigSingleRObject will work, then you can use the output just like any other SingleR object, but only using the single-cell option and not the cluster option (which is not really recommended anyway).