Package: svaNUMT 1.11.0

Ruining Dong

svaNUMT: NUMT detection from structural variant calls

svaNUMT contains functions for detecting NUMT events from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies NUMTs by nuclear-mitochondrial breakend junctions. The main function reports candidate NUMTs if there is a pair of valid insertion sites found on the nuclear genome within a certain distance threshold. The candidate NUMTs are reported by events.

Authors:Ruining Dong [aut, cre]

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svaNUMT.pdf |svaNUMT.html✨
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Bug tracker:https://github.com/papenfusslab/svanumt/issues

On BioConductor:svaNUMT-1.11.0(bioc 3.20)svaNUMT-1.10.0(bioc 3.19)

bioconductor-package

1 exports 1.08 score 84 dependencies

Last updated 2 months agofrom:b92b6fa8f7

Exports:numtDetect

Dependencies:abindAnnotationDbiaskpassassertthatBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIDelayedArraydplyrfansifastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngpwalignR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystringistringrStructuralVariantAnnotationSummarizedExperimentsystibbletidyselectUCSC.utilsutf8VariantAnnotationvctrswithrXMLXVectoryamlzlibbioc