Comrades, 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 instance. 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? Or? Curious to learn which way you folks are leaning ... Thanks! -steve 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
