Jean Fan

Addressed issues above. Additional issues to address: - At least 80% of man pages documenting exported objects must have runnable examples.The following pages do not: bwpca.Rd, knn.error.models.Rd, make.pagoda.app.Rd, pagoda.cluster.cells.Rd, pagoda.effective.cells.Rd,...

Addressed issues above. Additional issues to address: - checking dependencies in R code ... WARNING 'library' or 'require' calls not declared from: ‘Rook’ ‘extRemes’ ‘rjson’ 'library' or 'require' calls in...

- [ ] Tutorials need to have `library("scde")` added. - [x] Add http://pklab.med.harvard.edu/scde/pagoda.links.html link to let people browse sample results

- [ ] See Jen's recommendation - [ ] Use vertical bar or regex to choose multiple genes

Hi Poorya, You can always find more information about these methods with ?scde.expression.difference The data returned is a data frame with the following fields: \itemize{ \item{lb, mle, ub} {lower bound,...

Yes, if you have batch information, you can provide that into the groups parameter so that error-modeling is done in a batch-specific manner. Jean Fan, PhD Bioinformatics and Integrative Genomics...

Hi Marina, Hum, yes it is currently a little confusing. scde.expression.difference compares the cells you specify in the `groups` factor and the up and down directions are set based on...

Let me reopen this just so I have a reminder to update the documentation. Thanks again!

Hi Florian, Thanks for the thorough documentation of your issue. Can you please try to see if the error persists with `knn.error.models` in addition to `scde.error.models`? Also, can you please...

`papply` is just a wrapper function to call either `bplapply` or `mclapply`. So it seems like your cluster may be having trouble with either or both of those functions. Unfortunately...