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 OleÅ› 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel