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Bioconductor - StructuralVariantAnnotation (development version)

StructuralVariantAnnotation

This is the development version of StructuralVariantAnnotation; for the stable release version, see StructuralVariantAnnotation.

Variant annotations for structural variants

Bioconductor version: Development (3.22)

StructuralVariantAnnotation provides a framework for analysis of structural variants within the Bioconductor ecosystem. This package contains contains useful helper functions for dealing with structural variants in VCF format. The packages contains functions for parsing VCFs from a number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.

Author: Daniel Cameron [aut, cre] ORCID: 0000-0002-0951-7116 , Ruining Dong [aut] ORCID: 0000-0003-1433-0484

Maintainer: Daniel Cameron <daniel.l.cameron at gmail.com>

Citation (from within R, enter citation("StructuralVariantAnnotation")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("StructuralVariantAnnotation")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("StructuralVariantAnnotation")
Details biocViews Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation Version 1.25.0 In Bioconductor since BioC 3.9 (R-3.6) (6 years) License GPL-3 + file LICENSE Depends GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R (>= 4.1.0) Imports assertthat, Biostrings, pwalign, stringr, dplyr, methods, rlang, GenomicFeatures, IRanges, S4Vectors, SummarizedExperiment, GenomeInfoDb System Requirements URL See More Suggests ggplot2, devtools, testthat (>= 2.1.0), roxygen2, rmarkdown, tidyverse, knitr, ggbio, biovizBase, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19 Linking To Enhances Depends On Me svaNUMT, svaRetro Imports Me Suggests Me shiny.gosling Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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