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Hello!
Is there any easy way to know for a Bioconductor package which human genome builds it supports without reading the documentation manually? I have to identify dependencies that do not work on a particular genome build.
Thank you
Can you give an example of a package "not working" with a specific build? I would expect most packages to be de-coupled from specific builds because Bioconductor has various annotation resources e.g BSgenome, EnsDbs, TxDb etc which packages are encouraged to use, and that should abstract out many of the specific details of certain genome build i.e. a tool designed to work with a BSgenome will hopefully work with any BSgenome regardless of the organism or genome build. However it's certainly possible that packages are hardwired to use certain details. A concrete example would really help I think.
Thank you, Mike. As an example, the QDNAseq package is in essence genome-independent, as you've mentioned. However, to run on a particular genome build it requires a pre-computed dataset (bin annotations in this case) that is distributed as a separate package (QDNAseq.hg19). So basically it turns out that it will not work out of the box on
hg38for example as there is no "official"QDNAseq.hg38package.