I have developing an RNA-seq pipeline and one of the steps of this is to annotation my genes. I am using Ensembl IDs and I would like my query to return me "ensemblgeneid", "hgncid", "hgncsymbol","description". Indeed, I need this information for later performing Gene set enrichment analysis.
I have been having problems with BiomaRT being slow and timing out, as described in this post: https://support.bioconductor.org/p/122412/#122533
So I am thinking of changing to a different annotation package. The appear to be many out there: https://www.bioconductor.org/packages/release/data/annotation/
I need a package that would have b38 data for humans and would have "ensemblgeneid", "hgncid", "hgncsymbol","description" information. I have found the following (below)
Package Maintainer Title EnsDb.Hsapiens.v75 Johannes Rainer Ensembl based annotation package EnsDb.Hsapiens.v79 Johannes Rainer Ensembl based annotation package EnsDb.Hsapiens.v86 Johannes Rainer Ensembl based annotation package
However, I am concerned these packages may be outdated. Would anyone recommend a particular up to date package to replace BiomaRt? Has anyone had any experience similar to this?