Bioconductor version: Release (3.11)
StructuralVariantAnnotation 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] , Ruining Dong [aut]
Maintainer: Daniel Cameron <daniel.l.cameron at gmail.com>
Citation (from within R,
enter citation("StructuralVariantAnnotation")
):
To install this package, start R (version "4.0") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("StructuralVariantAnnotation")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("StructuralVariantAnnotation")
HTML | R Script | Structural Variant Annotation Package |
Reference Manual | ||
Text | NEWS |
biocViews | Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation |
Version | 1.4.0 |
In Bioconductor since | BioC 3.9 (R-3.6) (1.5 years) |
License | GPL-3 |
Depends | GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R (>= 3.6.0) |
Imports | assertthat, Biostrings, stringr, dplyr, methods, rlang |
LinkingTo | |
Suggests | BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat, roxygen2, covr, knitr, plyranges, ggbio, biovizBase, circlize, tictoc, GenomeInfoDb, IRanges, S4Vectors, SummarizedExperiment |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | StructuralVariantAnnotation_1.4.0.tar.gz |
Windows Binary | StructuralVariantAnnotation_1.4.0.zip |
macOS 10.13 (High Sierra) | StructuralVariantAnnotation_1.4.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/StructuralVariantAnnotation |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/StructuralVariantAnnotation |
Package Short Url | https://bioconductor.org/packages/StructuralVariantAnnotation/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.11 | Source Archive |
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