svaRetro

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see svaRetro.

Retrotransposed transcript detection from structural variants

Bioconductor version: 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 (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
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")

svaRetro Package HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, Coverage, DataImport, Genetics, Sequencing, Software, VariantAnnotation, VariantDetection

Version 1.0.0

In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)

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

System Requirements

URL

Bug Reports https://github.com/PapenfussLab/svaRetro/issues

Suggests TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, BiocStyle, plyranges, circlize, tictoc, IRanges, stats, SummarizedExperiment, rmarkdown

Linking To

Enhances

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Build Report Build Report

Package Archives

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

Source Package svaRetro_1.0.0.tar.gz

Windows Binary svaRetro_1.0.0.zip

macOS 10.13 (High Sierra) svaRetro_1.0.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/svaRetro

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/svaRetro

Bioc Package Browser https://code.bioconductor.org/browse/svaRetro/

Package Short Url https://bioconductor.org/packages/svaRetro/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.14 Source Archive