geoffschieb

Fate probabilities go forward in time, but ancestor probabilities go backward. On Mon, Jan 18, 2021 at 9:28 AM James Ashmore wrote: > Sorry for the naive question, but what...

Hi James, We used the log-normalized matrix for the OT computations. The truncated expression matrix was used in the regulatory regressions. We didn't do batch correction. This allowed us to...

Out of over 100 runs of 10x we threw out 1, which was very different than all our other samples. This was essentially a failed reaction. I'm not sure what...

Josh, have you tried with the new python build he is using from October 7? On Fri, Oct 18, 2019 at 5:30 AM Joshua Gould wrote: > I'm not sure...

This is described in the Methods S1 supplemental section of our paper. On Tue, May 7, 2019 at 6:38 AM frymor wrote: > In the new version you calculate the...

Dear Frymor, We have just released WOT 1.0 along with a tutorial: https://broadinstitute.github.io/wot/tutorial/ The gene scores calculations are explained in Notebook 1 and the STAR Methods of our paper (page...

Actually the cell sets are just loaded there ... not even computed! In Schiebinger et al 2019 we compute cell sets "by hand" through a mix of clustering and using...

Yes it makes sense that all the cell sets would be the same length when you run the command this way. The command selects the top x percent of cells...

The cluster 2 histogram is bimodal, so a cutoff of 8000 might be good. Not so sure about cluster 1. You can try visualizing the cells above different thresholds in...

Now I'm confused about your histograms because the values all look small in the table you just sent but the x-axis for the histogram has values of like 8000. The...