kieranrcampbell / embeddr Goto Github PK

Hi!

I have read your manuscript and am eager to try Embedrr. I am having some trouble installing the package, though, and was wondering if everything looks fine on your end.

I get the following error:

library(devtools)

install_github('davismcc/scater')
Downloading github repo davismcc/scater@master
Error in file(con, "wb") : cannot open the connection
In addition: Warning message:
In file(con, "wb") :
cannot open file '/tmp/RtmpGcdGRV/file16601f73f170.zip': No such file or directory.

install_github('kieranrcampbell/embeddr')
Downloading github repo kieranrcampbell/embeddr@master
Error in file(con, "wb") : cannot open the connection
In addition: Warning message:
In file(con, "wb") :
cannot open file '/tmp/RtmpGcdGRV/file166033aad563.zip': No such file or directory

Thanks!

Just noticed in the bioconductor repository that scater removed the celldist function from bioc-version 3_5 to 3_6. Is that going to be an issue when running the code with the updated scater library?

plot_in_pseudotime will call ggplot to color by cluster whether it's present in M or not - add check in future

I spent a decent amount of time trying to understand why I wasn't able to convert my dataframes to a SCESet object, until I realized scater had switched from SCESet objects to SingleCellExperiment objects. Would help if you could change that on the README (since it isn't completely straightforward to convert between the two). I understand that this is an old project though, so that's probably why.