Package: svaRetro 1.13.0
Ruining Dong
svaRetro: Retrotransposed transcript detection from structural variants
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.
Authors:
svaRetro_1.13.0.tar.gz
svaRetro_1.13.0.zip(r-4.5)svaRetro_1.13.0.zip(r-4.4)svaRetro_1.13.0.zip(r-4.3)
svaRetro_1.13.0.tgz(r-4.4-any)svaRetro_1.13.0.tgz(r-4.3-any)
svaRetro_1.13.0.tar.gz(r-4.5-noble)svaRetro_1.13.0.tar.gz(r-4.4-noble)
svaRetro_1.13.0.tgz(r-4.4-emscripten)svaRetro_1.13.0.tgz(r-4.3-emscripten)
svaRetro.pdf |svaRetro.html✨
svaRetro/json (API)
NEWS
| # Install 'svaRetro' in R: |
| install.packages('svaRetro', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/papenfusslab/svaretro/issues
On BioConductor:svaRetro-1.13.0(bioc 3.21)svaRetro-1.12.0(bioc 3.20)
dataimportsequencingannotationgeneticsvariantannotationcoveragevariantdetection
Last updated 4 months agofrom:4aeb18ce02. Checks:1 OK, 6 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 17 2025 |
| R-4.5-win | NOTE | Feb 17 2025 |
| R-4.5-linux | NOTE | Feb 17 2025 |
| R-4.4-win | NOTE | Feb 17 2025 |
| R-4.4-mac | NOTE | Feb 17 2025 |
| R-4.3-win | NOTE | Feb 17 2025 |
| R-4.3-mac | NOTE | Feb 17 2025 |
Exports:rtDetect
Dependencies:abindAnnotationDbiaskpassassertthatBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIDelayedArraydplyrfansifastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngpwalignR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystringistringrStructuralVariantAnnotationSummarizedExperimentsystibbletidyselectUCSC.utilsutf8VariantAnnotationvctrswithrXMLXVectoryaml
