[Bioc-devel] Plans for multi-feature SingleCellExperiment?

Steve Lianoglou m@|||ng||@t@honeypot @end|ng |rom gm@||@com
Tue Jan 22 23:18:11 CET 2019


Sorry if I'm out of the loop and have missed anything obvious.

I was curious what the plans are in the single-cell bioconductor-verse
to support single cell experiments that produce counts from different
feature-spaces, such as those produced by CITE-seq / REAP-seq, for

In these types of experiments, I'm pretty sure we want the counts
generated from those "features" (oligo-conjugated Antibodies, for
instance) to be kept in a separate space than the mRNA counts. I think
we would most  naturally want to put these in something like an
`assay()` matrix with a different (rowwise) dimmension than the gene
count matrix, but that can't work since all matrices in the assay()
list need to be of the same dimensions.

Another option might be to just add them as rows to the assay
matrices, but keep some type of feature space meta-information akin to
what `isSpike()` currently does;

or add a new slot to SingleCellExperiment to hold counts from
different feature spaces, perhaps?;

Or rely on something like a MultiAssayExperiment?


Curious to learn which way you folks are leaning ...


ps - sorry if this email came through twice, it was somehow magically
sent from an email address I don't have access to anymore.

Steve Lianoglou
Denali Therapeutics

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