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It seems like the functions in utils.R are all connected with the PCA function in that file. Is this PCA function actually used anywhere now? I saw a line using it that was commented out in the original VisualizeIntegration function (since removed), but I don't see it used anywhere else. It looks like we're just using the standard Seurat::UsePCA. Can we delete utils.R?

Should we consider adding doublet detection as an optional addition to SPEEDI? The relevant code can be run immediately after creation of the SeuratObject - something like this as a starting point:

# Load doublet package
library(scDblFinder)
# Find doublets
sc_obj <- as.Seurat(scDblFinder(as.SingleCellExperiment(sc_obj), samples = "sample"))
# See distribution of doublets in each sample
doublet_sc_obj <- subset(x = sc_obj, subset = scDblFinder.class %in% "doublet")
print(table(doublet_sc_obj$sample))
rm(doublet_sc_obj)
# Remove doublets
sc_obj <- subset(x = sc_obj, subset = scDblFinder.class %in% "singlet")

What was the source for the cc.gene.updated.mouse file?

Originally, in LoadReference, for a given reference, the function used data to load the reference data (e.g., data("kidneyref")). However, this doesn't seem to work with these reference data, as you get an error message like:

Warning message:
In data("kidneyref") : data set ‘kidneyref’ not found

Note that the data command does work for non-reference data distributed by SeuratData. This issue has been reported by other users: satijalab/seurat-data#53

We need to figure out how to successfully use these references. I will do some more testing and report back!

We should add a wrapper function so that users can run SPEEDI with a single function call (specifying data path, sample IDs, organism type, and tissue type).

This issue contains two steps:

1. Prepare SPEEDI as an R package (keeping in mind Bioconductor standards)
2. Submit SPEEDI to Bioconductor and go through the review process

Before SPEEDI is accepted to Bioconductor, we can provide instructions for how to install SPEEDI directly from GitHub. Reviewers may need to use this approach if we are still waiting for Bioconductor approval when we submit the paper.

Importantly, Bioconductor follows a release schedule where packages are released every ~six months (usually in April and October). If this schedule is completely at odds with the publication schedule, we may need to consider submitting to CRAN instead, but I think this is unlikely.