Viktor Petukhov

There were several problems with UMI correction, but now it should work. Please, check [the result](http://pklab.med.harvard.edu/viktor/dropest_paper/dropest_0.8.5.zip) I published for neurons_900. I fixed your config, so the pipeline reads non-corrected UMI...

> The weirdest thing is that, with every run of drpoEst, xml file gets cleared out. If you used xml from the same folder and the same name as in...

Hello, Sorry, but currently there is no way to run `droptag` on 10x v1.

Hi, 10x uses complicated way of library barcoding, so I'd recommend to use CellRanger instead of `droptag`. And then, you can still use `dropest` on the bam file, produced by...

Now if you have 10x without library tag, you can run it by using Split-seq config with adjusted parameters. To do so, add the following to `config/TagsSearch`: split_seq 0 16...

Hello, Thank you for looking at our tool. Indeed, it's possible to adopt the dropEst for this protocol, but it requires to write some code (changing config wouldn't be enough)....

Yes, please!

Thanks, Hannah! Please, see the pull request. > I just haven't had the time to implement any alternatives and glmnet seems to work ok most of the time. Again, if...

> Just pushed an addition for 1 above - add return_initial_assign = TRUE to use. One limitation is that it only returns information about the root level. Just in case,...

@samuel-marsh , yep, the PR would be very welcome :) @evanbiederstedt , there are actually surprisingly few [packages that import Cairo](https://cran.r-project.org/web/packages/Cairo/), I thought this number would be much higher.