Installation issue, updates to how it interacts with AUCell output

[zktuong]

Hi, thanks for the great package.

I ran into some issues with installation and decided to try and solve it. I've also adjusted how the functions accessing some slots in AUCell's output from regulonAUC@assays$data@listData$AUC to regulonAUC@assays@data@listData$AUC

I've also tried to move all the bits where you were loading the packages via require() or library() to @import.

I think it should install fine now and should work ok, but it's giving a couple of warning messages when installing. Some can be easily changed (e.g. just import tidyverse and not dplyr/plyr individually), but you can decide if you want to change it. Just printing the messages here for reference.

Warning: replacing previous import ‘AUCell::cbind’ by ‘SingleCellExperiment::cbind’ when loading ‘SCENIC’
Warning: replacing previous import ‘DT::JS’ by ‘Seurat::JS’ when loading ‘scFunctions’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘scFunctions’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘scFunctions’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘scFunctions’
Warning: replacing previous import ‘dplyr::failwith’ by ‘plyr::failwith’ when loading ‘scFunctions’
Warning: replacing previous import ‘dplyr::id’ by ‘plyr::id’ when loading ‘scFunctions’
Warning: replacing previous import ‘dplyr::summarize’ by ‘plyr::summarize’ when loading ‘scFunctions’
Warning: replacing previous import ‘dplyr::count’ by ‘plyr::count’ when loading ‘scFunctions’
Warning: replacing previous import ‘dplyr::desc’ by ‘plyr::desc’ when loading ‘scFunctions’
Warning: replacing previous import ‘dplyr::mutate’ by ‘plyr::mutate’ when loading ‘scFunctions’
Warning: replacing previous import ‘dplyr::arrange’ by ‘plyr::arrange’ when loading ‘scFunctions’
Warning: replacing previous import ‘dplyr::rename’ by ‘plyr::rename’ when loading ‘scFunctions’
Warning: replacing previous import ‘dplyr::summarise’ by ‘plyr::summarise’ when loading ‘scFunctions’
Warning: replacing previous import ‘DT::dataTableOutput’ by ‘shiny::dataTableOutput’ when loading ‘scFunctions’
Warning: replacing previous import ‘DT::renderDataTable’ by ‘shiny::renderDataTable’ when loading ‘scFunctions’

[FloWuenne]

Thanks so much, @zktuong for this great pull request. I haven't been updating this package in a while. This is really highly appreciated!

[zktuong]

All good. Happy to help!