A Build Ensembl-based annotation packages

A.1 Build EnsDb annotation packages from AnnotationHub

Code below demonstrates a quick way for creating an EnsDb annotation package using the AnnotationHub package and the GenomicFeatures::makeEnsembldbPackage() function. For comprehensive information on Ensembl-based annotation packages, please refer to Ensembldb on Bioconductor.

#'
#' EnsDb.Hsapiens.v92: 
#'
library(AnnotationHub)
library(ensembldb)
library(GenomicFeatures)
ah <- AnnotationHub(localHub=TRUE)
query(ah, c("hsapiens"))
edb <- ah[["AH60977"]] # select the source GRF from ensembl version 92
seqlevelsStyle(edb) <- "NCBI"
GenomicFeatures::makeEnsembldbPackage(
  ensdb=dbfile(dbconn(edb)),
  version="1.0.0",
  maintainer="Chao-Jen Wong <cwon2@fredhutch.org>",
  author="Chao-Jen Wong",
  destDir="/fh/fast/tapscott_s/CompBio/hg38")