Hi all, Briefly:
I'm looking to get guidance on how to handle data packages that support a suite of software packages I'd like to submit to bioconductor. More Detail: We (Genentech) have opened sourced some packages I've been developing internally for the past few years that facilitate the execution and exploration of gene set enrichment analyses. https://github.com/lianos/multiGSEA https://github.com/lianos/multiGSEA.shiny I will submit them to bioc "in the normal way", however my question is how I should do that because there are also data packages I have (that are Suggest(ed) by multiGSEA) that need to go in as well. Would these data go in as data packages or via AnnotationHub? multiGSEA provides convenience wrappers to retrieve genesets from different sources. One of these resources is the gene set collections made available by MSigDB. Using multiGSEA, a user can get the hallmark and c2 gene set collections like so: ``` library(multiGSEA) gdb.human <- getMSigGeneSetDb(c("h", "c2"), "human") gdb.mouse <- getMSigGeneSetDb(c("h", "c2"), "mouse") ``` These function calls check if the following data packages are installed and retrieve the appropriate gene sets if so (otherwise they raise an error): https://github.com/lianos/GeneSetDb.MSigDB.Hsapiens.v61 https://github.com/lianos/GeneSetDb.MSigDB.Mmusculus.v61 I've created these data packages so that they approximate what I think looks like something suitable for AnnotationHub (ie. with working inst/scripts/make-data.R scripts). These data packages start with MSigDB's gene set *xml files (ie. 'msigdb_v6.1.xml') and convert them into multiGSEA::GeneSetDb *.rds objects which are then used by the multiGSEA and multiGSEA.shiny packages. I'm curious how to proceed from here? Thanks, -steve ps: I know bioc looks down on not using "foundational" bioc classes, so we can have this discussion during pkg review, but a GeneSetDb object is a reimagined take on the GSEABase::GeneSetCollection. Unfortunately the latter just wasn't providing the functionality I wanted for how I felt like I wanted to interact with collections of genesets ... mulitGSEA provides methods to convert a GeneSetCollection to a GeneSetDb, and vice versa -- Steve Lianoglou Bioinformatics Scientist Cancer Immunology Genentech _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
