svaRetro
Retrotransposed transcript detection from structural variants
Bioconductor version: Release (3.20)
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("svaRetro")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Annotation, Coverage, DataImport, Genetics, Sequencing, Software, VariantAnnotation, VariantDetection |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 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 |
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
Follow Installation instructions to use this package in your R session.
| Source Package | svaRetro_1.12.0.tar.gz |
| Windows Binary (x86_64) | svaRetro_1.12.0.zip (64-bit only) |
| macOS Binary (x86_64) | svaRetro_1.12.0.tgz |
| macOS Binary (arm64) | svaRetro_1.11.0.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 |