pkharchenko

we'll try to move this to ggplot in the next release, meanwhile, you can skip the most expensive recalculation by passing back cc parameter: x On Feb 1, 2018, at...

Thanks for the hint, Ivan! If others keep encountering this error, please share an example dataset to help us replicate it. Thank you, -peter. > On May 23, 2018, at...

colDeltaCor functions calculate for each cell (column E_i of a matrix E) correlation between E-E_i and D_i (difference vector expected from velocity of the cell I). colDeltaSqrt and Log10 variants...

Yes, the if there are two identical cells (i.e. two all-0 E columns), that would lead to NAs … most likely those entries in the output matrix can be simply...

Thank you, Philipp for the suggested patch. Unfortunately, I can’t seem to replicate the error. As suggested, I’ve ran the SCG71 tutorial example (http://pklab.med.harvard.edu/velocyto/notebooks/R/SCG71.nb.html) on several R versions that I...

Can you please paste the error traceback() and sessionInfo(). Thank you, -peter. > On Jul 22, 2019, at 17:33, mbassalbioinformatics wrote: > > Having the same issue and would appreciate...

This is more of a question for the Seurat list, but we'll try to add an example when we update tutorials.

It’s not strictly necessary to select “cluster-distinguishing genes - it’s a recommended step. If different clusters in your dataset represent different points in the dynamic process, this will likely result...

Yes, unfortunately we haven’t had the time or resources to maintain it, to keep up with evolving dependencies, especially across platforms. Obviously the docker still works if you don’t want...

It shouldn’t take that long - the scaling is essentially linear with respect to the number of genes and something like n*log(n) for cells. I would first check to make...