R/qtl2bioc is part of R/qtl2. It uses Bioconductor facilities to obtain the set of mouse genes in a region. While the functions within R/qtl2bioc could logically be included within qtl2, we've kept it separate in order to reduce package dependencies for those not interested in making use of the Bioconductor features.
To install R/qtl2bioc, first install the Bioconductor packages GenomicRanges and AnnotationHub:
install.packages("BiocManager")
BiocManager::install(c("GenomicRanges", "AnnotationHub"))Next, install R/qtl2bioc from r-universe:
install.packages("qtl2bioc", repos=c("https://rqtl.r-universe.dev",
"https://cloud.r-project.org"))Alternatively, install the remotes package
and use remotes::install_github() to install R/qtl2bioc from its
Github repository.
install.packages("remotes")
library(remotes)
install_github("rqtl/qtl2bioc")The R/qtl2bioc package contains two
key functions, grab_ensembl(), for downloading the
Ensembl gene annotations, and
create_ensembl_query_func(), for creating a query function to
grab gene records for a given region.