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
Browse package contents
Package details |
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| Bioconductor views | Annotation DataRepresentation GenomeAnnotation GenotypingArray Infrastructure Sequencing |
| Maintainer | |
| License | GPL-3 |
| Version | 1.21.0 |
| URL | https://github.com/Bioconductor/VariantExperiment |
| Package repository | View on GitHub |
| Installation |
Install the latest version of this package by entering the following in R:
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