[Bioc-devel] A pie in the sky idea/wish: DifferentialExpressionSummarizedExperiment clas

[Leonardo Collado Torres]

Hi,

The tidybulk [1] workshop yesterday and Sean Davis & Levi Waldron's &
Benjamin Haibe-Kains workshop [2] got me thinking today in the morning
of a pie in the sky idea. Just like SummarizedExperiment has helped
many of us to organize our data, it would be awesome if there was
something like a DifferentialExpressionSummarizedExperiment class or
something like that. I know that Andrzej Oleś did a lot of work in
DEFormats, and it seems like now the Stefano Mangiola & Maria Doyle
are going through a similar effort of adding support to both edgeR and
DESeq2 (and limma??) outputs. I went through something similar with
regionReport, and well, if there was a common output object type or
functions that converted the current outputs into a common format,
that might make building upon these tools (and other DE packages) much
easier. I bet that you could submit a CZI EOSS application for
supporting the refactoring process & defining the output format.

Though maybe you already tried doing this in the past and I'm simply
unaware of it. Anyway, just an idea/wish.

Best,
Leo

PS I'd post this on Slack, but I'm not sure everyone's active there.

[1] http://bioconductor.org/packages/release/bioc/html/tidybulk.html
and https://twitter.com/Bioconductor/status/1287855026627518464?s=20
[2] https://twitter.com/Bioconductor/status/1287764789586989057?s=20
[3] http://bioconductor.org/packages/release/bioc/html/DEFormats.html