svaRetro

This is thedevelopment version of svaRetro; for the stable release version, seesvaRetro.

Retrotransposed transcript detection from structural variants

DOI: 10.18129/B9.bioc.svaRetro

Bioconductor version: Development (3.23)

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] ORCID: 0000-0003-1433-0484

Maintainer: Ruining Dong <lnyidrn at gmail.com>

Citation (from within R, entercitation("svaRetro")):

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))    install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("svaRetro")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation,Coverage,DataImport,Genetics,Sequencing,Software,VariantAnnotation,VariantDetection
Version	1.17.0
In Bioconductor since	BioC 3.14 (R-4.1) (4 years)
License	GPL-3 + file LICENSE
Depends	GenomicRanges,rtracklayer,BiocGenerics,StructuralVariantAnnotation, R (>= 4.0)
Imports	VariantAnnotation,assertthat,Biostrings,stringr,dplyr, methods,rlang,S4Vectors,Seqinfo,GenomeInfoDb,GenomicFeatures, 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
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Build Report	Build Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source Package
Windows Binary (x86_64)
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/
Package Downloads Report	Download Stats

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