Adding a new dataset: scRNA-Seq + single-cell proteomics (SCoPE2)

cvanderaa commented 3 years ago

Hello,

@lgatto and I would like to collaborate on the SingleCellMultiModal project. I here submit a first instance of a PR, but please do not merge yet! I'm following the Contributing-guidelines.Rmd. Details about the data can be found in the documentation R/SCoPE2.R.

TODO

[x] Discuss the name of the function + name of the DataType. Note that SCoPE2 is the name of the protocol for performing single-cell proteomics. Decision: keep SCoPE2 as the name of the technique (cf seqFISH), but name DataType after the cell type (macrophage_differentiation in this case).
[x] Combine the scRNA-seq data in a single assay (HDF5-backend?)
[x] Write a vignette
[x] Extend the metadata.csv
[x] Upload files to ExperimentHub
[x] Check everything is working

cvanderaa commented 3 years ago

I think it's good on my side. @LiNk-NY, let me know if you have additional remarks.

LiNk-NY commented 3 years ago

Hi Chris, @cvanderaa

Thanks for your contribution! I made some minor changes to the main function. I've tested it locally and it works well. Let's keep an eye out on the Bioconductor builds just in case: https://bioconductor.org/packages/devel/data/experiment/html/SingleCellMultiModal.html

Best, Marcel

cvanderaa commented 3 years ago

Excellent ! Thanks for the code review and for merging!

waldronlab / SingleCellMultiModal

Adding a new dataset: scRNA-Seq + single-cell proteomics (SCoPE2) #26

TODO