Package: epialleleR 1.13.0

Oleksii Nikolaienko

epialleleR: Fast, Epiallele-Aware Methylation Caller and Reporter

Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls and reports cytosine methylation as well as frequencies of hypermethylated epialleles at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Among other things, this package can also extract methylation patterns and assess allele specificity of methylation.

Authors:Oleksii Nikolaienko [aut, cre]

epialleleR_1.13.0.tar.gz
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epialleleR.pdf |epialleleR.html✨
epialleleR/json (API)
NEWS

Peer review:

Bug tracker:https://github.com/bbcg/epialleler/issues

On BioConductor:epialleleR-1.13.0(bioc 3.20)epialleleR-1.12.0(bioc 3.19)

bioconductor-package

12 exports 1.51 score 72 dependencies

Last updated 2 months agofrom:356cd8e15b

Exports:callMethylationextractPatternsgenerateAmpliconReportgenerateBedEcdfgenerateBedReportgenerateCaptureReportgenerateCytosineReportgenerateMhlReportgenerateVcfReportpreprocessBampreprocessGenomesimulateBam

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurldata.tableDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsVariantAnnotationvctrsXMLXVectoryamlzlibbioc