Add qs and SeuratObject to renv

[sjspielman]

From https://github.com/AlexsLemonade/training-modules/pull/990/changes#r3219607976

While adding qs I realized we need Seurat too. I did not want to put Seurat into our renv, but I think it's reasonable to put SeuratObject in. The only piece of code in the reference conversion script that needs the full Seurat package is as.SingleCellExperiment(), so we can just construct it manually with e.g.

sce <- SingleCellExperiment(
  assays = list(counts = mm_mets[["RNA"]]$counts)
)
stopifnot("bad conversion" = mm_mets@meta.data)
colData(sce) <- DataFrame(mm_mets@meta.data)

I think this is a good middle ground but it's not the most lightweight, so let me know if you prefer to not put this in renv at all.
While I was here I also update the renv settings json to get it to stop telling me to snapshot ScPCAr which we don't want snapshotted.

[jashapiro]

Are we not installing this because it is too heavy with dependencies? We already have a lot in the repo, so I would not expect too many extra things to be pulled in.

[sjspielman]

No, just neither of us thought it belonged in renv necessarily when I filed that PR. We can put it in though, it won't be that heavy.

[jashapiro]

From https://github.com/AlexsLemonade/training-modules/pull/990/changes#r3219607976

While adding qs I realized we need Seurat too. I did not want to put Seurat into our renv, but I think it's reasonable to put SeuratObject in. The only piece of code in the reference conversion script that needs the full Seurat package is as.SingleCellExperiment(), so we can just construct it manually with e.g.

sce <- SingleCellExperiment(
  assays = list(counts = mm_mets[["RNA"]]$counts)
)
stopifnot("bad conversion" = mm_mets@meta.data)
colData(sce) <- DataFrame(mm_mets@meta.data)

I think this is a good middle ground but it's not the most lightweight, so let me know if you prefer to not put this in renv at all. While I was here I also update the renv settings json to get it to stop telling me to snapshot ScPCAr which we don't want snapshotted.

We might as well add Seurat, I guess? People are gonna want it no matter what we do.

[jashapiro]

👍🏼