svaRetro
Retrotransposed transcript detection from structural variants
Bioconductor version: 3.23 · Package version: 1.18.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("svaRetro")Details
| Maintainer | Ruining Dong <lnyidrn@gmail.com> |
| Author | Ruining Dong [aut, cre] (ORCID: <https://orcid.org/0000-0003-1433-0484>) |
| License | GPL-3 + file LICENSE |
| Bug Reports | https://github.com/PapenfussLab/svaRetro/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, Coverage, DataImport, Genetics, Sequencing, Software, VariantAnnotation, VariantDetection |
| Package Short Url | https://bioconductor.org/packages/svaRetro/ |
Citation
From within R, enter citation("svaRetro"):
Ruining Dong. svaRetro: Retrotransposed transcript detection from structural variants. doi:10.18129/B9.bioc.svaRetro, R package version 1.18.0, https://bioconductor.org/packages/svaRetro.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | svaRetro_1.18.0.tar.gz |
| Windows binary (x86_64) | svaRetro_1.18.0.zip |
| macOS binary (arm64) | svaRetro_1.18.0.tgz |
| macOS binary (x86_64) | svaRetro_1.18.0.tgz |
Dependencies
Depends: GenomicRanges, rtracklayer, BiocGenerics, StructuralVariantAnnotation, R (>= 4.0)
Imports: VariantAnnotation, AnnotationDbi, assertthat, Biostrings, stringr, dplyr, methods, rlang, S4Vectors, Seqinfo, GenomeInfoDb, GenomicFeatures, utils
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