lshep

You'll need to include man pages for your exported functions. It looks like you have roxygen markup in your R files; perhaps you forgot to run devtools::document() and commit the...

I will also add that in general it is normally not overly complicated to incorporate use of SummarizedExperiment in functions, for example, you could continue to support matrix like objects...

@ibkstore Do you plan on revising the package to the suggestions from @hpages , @vjcitn and myself?

We will close this issue for now. please comment back here when you are ready to continue and we will reopen the issue.

Do the histories of the repositories not match? Did you not work in the same repository as before?

You should familiarize yourself with git and git commands. Also this [previous comment](https://github.com/Bioconductor/Contributions/issues/3018#issuecomment-1665711628) links to a git workflow for pushing to git.bioconductor.org and indicates that you should set up your...

The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel. To use the git.bioconductor.org repository, we need an 'ssh' key to associate with...

I just tried to build locally and I get ``` Quitting from lines 383-399 [precast_k2] (visiumStitched.Rmd) Error: processing vignette 'visiumStitched.Rmd' failed with diagnostics: undefined columns selected --- failed re-building ‘visiumStitched.Rmd’...

indeed. I shall try again.

Its less than 10 min but not by much at 8 min 37 sec . Finding ways to reduce the time would be beneficial. As long as any exported function...