svaRetro
This is the development version of svaRetro; for the stable release version, see svaRetro.
Retrotransposed transcript detection from structural variants
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| svaRetro Package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Annotation, Coverage, DataImport, Genetics, Sequencing, Software, VariantAnnotation, VariantDetection |
| Version | 1.19.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 years) |
| License | GPL-3 + file LICENSE |
| Depends | GenomicRanges, rtracklayer, BiocGenerics, StructuralVariantAnnotation, R (>= 4.0) |
| Imports | VariantAnnotation, AnnotationDbi, 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, org.Hs.eg.db, 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_1.19.0.tar.gz |
| Windows Binary (x86_64) | svaRetro_1.19.0.zip |
| macOS Binary (big-sur-x86_64) | svaRetro_1.19.0.tgz |
| macOS Binary (sonoma-arm64) | svaRetro_1.19.0.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 |