Bioconductor/VariantExperiment: A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

VariantExperiment is a Bioconductor package for saving data in VCF/GDS format into RangedSummarizedExperiment object. The high-throughput genetic/genomic data are saved in GDSArray objects. The annotation data for features/samples are saved in DelayedDataFrame format with mono-dimensional GDSArray in each column. The on-disk representation of both assay data and annotation data achieves on-disk reading and processing and saves memory space significantly. The interface of RangedSummarizedExperiment data format enables easy and common manipulations for high-throughput genetic/genomic data with common SummarizedExperiment metaphor in R and Bioconductor.

Getting started

Package details

Bioconductor views Annotation DataRepresentation GenomeAnnotation GenotypingArray Infrastructure Sequencing
Maintainer
LicenseGPL-3
Version1.7.1
URL https://github.com/Bioconductor/VariantExperiment
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("Bioconductor/VariantExperiment")
Bioconductor/VariantExperiment documentation built on May 27, 2021, 1:30 a.m.