svaRetro

DOI: 10.18129/B9.bioc.svaRetro    

This is the development version of svaRetro; to use it, please install the devel version of Bioconductor.

Retrotransposed transcript detection from structural variants

Bioconductor version: Development (3.14)

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 "4.1") and enter:

if (!requireNamespace("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

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

browseVignettes("svaRetro")

 

HTML R Script svaRetro Package
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Annotation, Coverage, DataImport, Genetics, Sequencing, Software, VariantAnnotation, VariantDetection
Version 0.99.23
In Bioconductor since BioC 3.14 (R-4.1)
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
Links To Me
Build Report  

Package Archives

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

Source Package svaRetro_0.99.23.tar.gz
Windows Binary svaRetro_0.99.23.zip
macOS 10.13 (High Sierra) svaRetro_0.99.23.tgz
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/
Package Downloads Report Download Stats

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