svaRetro
This is thereleased version of svaRetro; for the devel version, seesvaRetro.
Retrotransposed transcript detection from structural variants
Bioconductor version: Release (3.22)
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("svaRetro")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("svaRetro")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Annotation,Coverage,DataImport,Genetics,Sequencing,Software,VariantAnnotation,VariantDetection |
| Version | 1.15.1 |
| In Bioconductor since | BioC 3.14 (R-4.1) (4 years) |
| License | GPL-3 + fileLICENSE |
| 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 |
See More
| 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 | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | svaRetro_1.15.1.tar.gz |
| Windows Binary (x86_64) | svaRetro_1.15.1.zip |
| macOS Binary (x86_64) | svaRetro_1.15.1.tgz |
| macOS Binary (arm64) | svaRetro_1.15.1.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 |