svaRetro

DOI: 10.18129/B9.bioc.svaRetro    

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

Retrotransposed transcript detection from structural variants

Bioconductor version: Development (3.17)

svaRetro contains functions for detecting retrotransposed transcripts (RTs) from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies RTs by exon-exon junctions and insertion sites. The candidate RTs are reported by events and annotated with information of the inserted transcripts.

Author: Ruining Dong [aut, cre]

Maintainer: Ruining Dong <lnyidrn at gmail.com>

Citation (from within R, enter citation("svaRetro")):

Installation

To install this package, start R (version "4.3") and enter:

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

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

BiocManager::install("svaRetro")

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

Documentation

PDF   Reference Manual

Details

biocViews Annotation, Coverage, DataImport, Genetics, Sequencing, Software, VariantAnnotation, VariantDetection
Version 1.5.0
In Bioconductor since BioC 3.14 (R-4.1) (1 year)
License GPL-3 + file LICENSE
Depends GenomicRanges, rtracklayer, BiocGenerics, StructuralVariantAnnotation, R (>= 4.0)
Imports VariantAnnotation, assertthat, Biostrings, stringr, dplyr, methods, rlang, GenomicFeatures, GenomeInfoDb, S4Vectors, utils
LinkingTo
Suggests TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, BiocStyle, plyranges, circlize, tictoc, IRanges, stats, SummarizedExperiment, rmarkdown
SystemRequirements
Enhances
URL
BugReports https://github.com/PapenfussLab/svaRetro/issues
Depends On Me
Imports Me
Suggests Me
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Build Report  

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/svaRetro
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/svaRetro
Package Short Url https://bioconductor.org/packages/svaRetro/
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