Missing links for .rds files

[jonmenard]

Hello, I am following the Readme to host my own instance of the webapp. However I only see download links for the .Rdata files. Is there somewhere I can download, or do I need to process something?

allCells_subsample_rds <- "./data/scMuscle_subsampled_mm10_v1-1.rds"
allCells_rds <- "./data/scMuscle_mm10_v1-1.rds"
myoCells_rds <- "./data/myo_slim_seurat_v1-1.rds"
vis_rds <- "./data/vis_slim_v1.rds"

Thanks in advance!

[mckellardw]

Great question - if I remember correctly, we switched from .Rdata to .rds for the web app because of the faster loading speeds. Those .RData files on zenodo are the same data, just in a different format. 2 options for you-

1. You can download the .rds formatted files directly from our web app (http://scmuscle.bme.cornell.edu/) - though as I am guessing you already know, it has very limited bandwidth.

2. You can load those .RData files into R and re-save them as .rds - it should work, but feel free to post any more issues here!

[jonmenard]

Thanks for the response! Do you have a mapping of the .Rdata to .rds. I see 3 .Rdata in the code (4 from the https://datadryad.org/dataset/doi:10.5061/dryad.t4b8gtj34 however) and 4 .rds files

To add to this I see a script generate_subsampled_scMuscle.R should I be using that to process the files into .rds

[mckellardw]

The CellChat results (scMuscle_cellchat_v1-1.RData) are not used in the shiny app, so you don't need to worry about that one