Hi Teemu Daniel, Those packages were developed before ExperimentHub.
Please follow the current standard for experiment data packages at https://bioconductor.org/packages/release/bioc/vignettes/ExperimentHub/inst/doc/ExperimentHub.html You may want to take a look at curatedTCGAData as an example (disclaimer: I developed the package). It is advisable to split the resources into more modular components, e.g., colData, sampleMap, data assays rather than distribute serialized MultiAssayExperiment objects. IMO, there should be no compatibility issues as the changes would only affect the underlying code and not the user interface. Best regards, Marcel On 11/24/22 1:57 AM, Daniel Laajala wrote: > Dear Bioconductor devs, > > thanks for all the hard work. Regarding if there's any leeway in how > ExperimentData-packages are structured: > > We started working a few years back on a "curatedPCaData" R-package for > curating prostate cancer multi-'omics datasets. We followed the structure of > a family of similar packages, e.g. readily on bioc: > https://bioconductor.org/packages/release/data/experiment/html/curatedBreastData.html > https://bioconductor.org/packages/release/data/experiment/html/curatedOvarianData.html > > With the data in a satisfactory form, we were now hoping to submit the > package to Bioconductor. However, due to the size of > MultiAssayExperiment-objects, the package is auto-rejected: > https://github.com/Bioconductor/Contributions/issues/2804 > > The data-raw/-files we can discard, as we provided these just for extra user > convenience. > However, the mae_*.rda files are essential MultiAssayExperiment objects (as a > standard format for multi-'omics in Bioc), but these are right now too large > for the bot. > > Reading the package structure instructions, we were under the impression that > this old structure for ExperimentData would still be ok for Bioconductor; the > package passed checks (R CMD check and BiocCheck) with minor NOTEs. Our > current GitHub is at: > https://github.com/Syksy/curatedPCaData > > Our package already has citations (with code provided there-in for extracting > and processing relevant data from the package), has been forked, has > collaborators using it as-is, etc, so revamping it to e.g. > ExperimentHub-structure would most likely cause quite major compatibility > issues. > > > Would there be any chance of approaching Bioconductor with the package > roughly in its current format inspired by these older curated-packages, even > if it is not in the updated ideal ExperimentData-format? > > Kind regards, > Teemu Daniel Laajala > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or...{{dropped:4}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
