add get_pseudobulk API

[stemangiola]

We have suitable available for the whole atlas, we should built a function that delivers those to the user

The interface would look like

metadata |>
   filter(...) |>
   get_pseudobulk()

The backend would look like

function(my_tibble){

   # select sample_ from tibble

  # Download pre-made pseudobulk from the cloud

  # bind
  
  # return

}

[myushen]

What do we want to download here after selecting sample_? SCE counts and cpm for selected sample_?

[stemangiola]

What do we want to download here after selecting sample_? SCE counts and cpm for selected sample_?

We would have SummarizedExperiments in the cloud (instead of SingleCellExperiment for single-cell). Those could include raw counts, and cpm/normalised assays (?).

[myushen]

so we don't have SummarizedExperiments in the cloud yet but plan to generate them for selected samples? Would converting SCE to SummarizedExperiments work in this case?

[stemangiola]

so we don't have SummarizedExperiments in the cloud yet but plan to generate them for selected samples? Would converting SCE to SummarizedExperiments work in this case?

we have them locally, they would not be generated on the flight, but recalculated. Instead of selecting the face based on cells, we would select five based on samples and cell types.

Sample 1 cell type epithelial = 1 observation = 1 file

Have a look to my updated strategy

#136 (comment)