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GenomicsDB / GenomicsDB-R

Experimental R bindings to the native GenomicsDB library
GNU General Public License v2.0
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genomics genomics-data genomicsdb r

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GenomicsDB-R

Experimental R bindings to the native GenomicsDB library. Only queries are supported for now. For ingestion, use GenomicsDB native command line tool vcf2genomicsdb or gatk GenomicsDBImport.

Installation

Prerequisites

See GenomicsDB build/install for a docker or a scripted install of GenomicsDB for MacOS and Linux based systems. Use the installed GenomicsDB path as input to GenomicsDB-R configuration. See <path_to_genomicsdb> below.

Installation from Github using remotes

From R/RStudio
library(remotes)
remotes::install_github("GenomicsDB/GenomicsDB-R", ref="<github_branch>", configure.args="--with-genomicsdb=<path_to_genomicsdb>")