Edits from workshop discussion meeting

[mblue9]

No description provided.

[mblue9]

Testing out the merged PR now, should I add tidysc as package here?

   Error: processing vignette 'tidytranscriptomics_case_study.Rmd' failed with diagnostics:
   there is no package called 'tidysc'

[stemangiola]

Testing out the merged PR now, should I add tidysc as package here?

   Error: processing vignette 'tidytranscriptomics_case_study.Rmd' failed with diagnostics:
   there is no package called 'tidysc'

I am incorporating the function now. I will push the changes very soon

[mblue9]

Ok great, one other thing I notice at the moment is that we still have some Seurat commands for the bit below in the vignette, are there Bioconductor equivalents we could use instead?

It is then possible to perform analyses on these gamma delta T cells by simply chaining further commands, such as below.

sce_obj_gamma_delta |>

  # Reanalyse
  NormalizeData(assay="RNA") |>
  FindVariableFeatures( nfeatures = 100, assay="RNA") |>
  SplitObject(split.by = "file") |>
  RunFastMNN(assay="RNA") |>
  RunUMAP(reduction = "mnn", dims = 1:20) |>
  FindNeighbors( dims = 1:20, reduction = "mnn") |>
  FindClusters( resolution = 0.3)

[stemangiola]

I have the feeling we solved this problem with one of the BioC workshops. With BioC data reanalysis.

[mblue9]

Don't see it in iscb2022 one but look like it's in
this rpharma2021 one https://tidytranscriptomics-workshops.github.io/rpharma2021_tidytranscriptomics/articles/tidytranscriptomics.html#part-2-single-cell-rna-sequencing-with-tidysinglecellexperiment-1
and similar ismb2021 https://tidytranscriptomics-workshops.github.io/ismb2021_tidytranscriptomics/articles/tidytranscriptomics.html#part-2-single-cell-rna-sequencing-with-tidysinglecellexperiment-1
If that's it are you able to pull out what commands we should include here?

[mblue9]

Besides above I think the main thing we need is a bit more explanation for the pseudobulk part on what's being done and the code as for prerequisites we only require basic tidyverse/single cell so some more text/comments e.g. on the steps and nest, map, map2, map_int would be good. If you could add a couple more comments I could flesh out text once the code runs (need above tidysc bit).