| .CpG.dinuc.unify |
Source code
|
| .CpG.dinuc.unifyOld |
Source code
|
| .adjlim |
Source code
|
| .check.dbdir |
Source code
|
| .check.pipeline.list |
Source code
|
| .checkTabixFileExists |
Source code
|
| .cluster |
Source code
|
| .decodeShortSlotNames |
Source code
|
| .dist.cor |
Source code
|
| .encodeShortSlotNames |
Source code
|
| .formatShortSlotValues |
Source code
|
| .formatTabixHeader |
Source code
|
| .methSeg |
Source code
|
| .pcaPlot |
Source code
|
| .pcaPlotT |
Source code
|
| .plotCorrelation |
Source code
|
| .procBismarkCoverage |
Source code
|
| .procBismarkCytosineReport |
Source code
|
| .readTableFast |
Source code
|
| .selectByOverlap |
Source code
|
| .setMethylDBNames |
Source code
|
| .structureAMPoutput |
Source code
|
| .structureGeneric |
Source code
|
| .write.table.noSci |
Source code
|
| FUN |
Source code
|
| PCASamples |
Man page
|
| PCASamples,methylBase-method |
Man page
|
| PCASamples,methylBaseDB-method |
Man page
|
| SLIMfunc |
Source code
|
| [,methylBase,ANY,ANY,ANY-method |
Man page
|
| [,methylBaseDB,ANY,ANY,ANY-method |
Man page
|
| [,methylDiff,ANY,ANY,ANY-method |
Man page
|
| [,methylDiffDB,ANY,ANY,ANY-method |
Man page
|
| [,methylRaw,ANY,ANY,ANY-method |
Man page
|
| [,methylRawDB,ANY,ANY,ANY-method |
Man page
|
| adjust.methylC |
Man page
Source code
|
| adjustMethylC |
Man page
|
| adjustMethylC,methylRaw,methylRaw-method |
Man page
|
| adjustMethylC,methylRawDB,methylRawDB-method |
Man page
|
| adjustMethylC,methylRawList,methylRawList-method |
Man page
|
| adjustMethylC,methylRawListDB,methylRawListDB-method |
Man page
|
| annotate.WithFeature |
Man page
Source code
|
| annotate.WithFeature.Flank |
Man page
Source code
|
| annotate.WithGenicParts |
Man page
Source code
|
| applyTbxByChr |
Source code
|
| applyTbxByChunk |
Source code
|
| applyTbxByOverlap |
Source code
|
| assocComp |
Man page
Source code
|
| bedgraph |
Man page
|
| bedgraph,methylDiff-method |
Man page
|
| bedgraph,methylDiffDB-method |
Man page
|
| bedgraph,methylRaw-method |
Man page
|
| bedgraph,methylRawDB-method |
Man page
|
| bedgraph,methylRawList-method |
Man page
|
| bedgraph,methylRawListDB-method |
Man page
|
| calculateDiffMeth |
Man page
|
| calculateDiffMeth,methylBase-method |
Man page
|
| calculateDiffMeth,methylBaseDB-method |
Man page
|
| calculateDiffMethDSS |
Man page
|
| calculateDiffMethDSS,methylBase-method |
Man page
|
| callDML2 |
Source code
|
| catsub2tabix |
Source code
|
| checkTabixHeader |
Source code
|
| clusterSamples |
Man page
|
| clusterSamples,methylBase-method |
Man page
|
| clusterSamples,methylBaseDB-method |
Man page
|
| colSds |
Source code
|
| compute.mean |
Source code
|
| compute.waldStat |
Source code
|
| dataSim |
Man page
Source code
|
| definition |
Source code
|
| densityFind |
Source code
|
| df2tabix |
Source code
|
| diagPlot |
Source code
|
| diffMethPerChr |
Man page
|
| diffMethPerChr,methylDiff-method |
Man page
|
| diffMethPerChr,methylDiffDB-method |
Man page
|
| dispersion.shrinkage |
Source code
|
| error |
Source code
|
| est.prior.logN |
Source code
|
| extract |
Man page
|
| extract,methylBase,ANY-method |
Man page
|
| extract,methylBaseDB,ANY-method |
Man page
|
| extract,methylDiff,ANY-method |
Man page
|
| extract,methylDiffDB,ANY-method |
Man page
|
| extract,methylRaw,ANY-method |
Man page
|
| extract,methylRawDB,ANY-method |
Man page
|
| filterByCoverage |
Man page
|
| filterByCoverage,methylRaw-method |
Man page
|
| filterByCoverage,methylRawDB-method |
Man page
|
| filterByCoverage,methylRawList-method |
Man page
|
| filterByCoverage,methylRawListDB-method |
Man page
|
| fread.gzipped |
Source code
|
| get.methylDiff |
Man page
Source code
|
| getAssembly |
Man page
|
| getAssembly,methylBase-method |
Man page
|
| getAssembly,methylBaseDB-method |
Man page
|
| getAssembly,methylDiff-method |
Man page
|
| getAssembly,methylDiffDB-method |
Man page
|
| getAssembly,methylRaw-method |
Man page
|
| getAssembly,methylRawDB-method |
Man page
|
| getContext |
Man page
|
| getContext,methylBase-method |
Man page
|
| getContext,methylBaseDB-method |
Man page
|
| getContext,methylDiff-method |
Man page
|
| getContext,methylDiffDB-method |
Man page
|
| getContext,methylRaw-method |
Man page
|
| getContext,methylRawDB-method |
Man page
|
| getCorrelation |
Man page
|
| getCorrelation,methylBase-method |
Man page
|
| getCorrelation,methylBaseDB-method |
Man page
|
| getCoverageStats |
Man page
|
| getCoverageStats,methylRaw-method |
Man page
|
| getCoverageStats,methylRawDB-method |
Man page
|
| getDBPath |
Man page
|
| getDBPath,methylBaseDB-method |
Man page
|
| getDBPath,methylDiffDB-method |
Man page
|
| getDBPath,methylRawDB-method |
Man page
|
| getDBPath,methylRawListDB-method |
Man page
|
| getData |
Man page
|
| getData,methylBase-method |
Man page
|
| getData,methylBaseDB-method |
Man page
|
| getData,methylDiff-method |
Man page
|
| getData,methylDiffDB-method |
Man page
|
| getData,methylRaw-method |
Man page
|
| getData,methylRawDB-method |
Man page
|
| getFeatsWithTargetsStats |
Man page
Source code
|
| getFlanks |
Man page
Source code
|
| getMembers |
Man page
Source code
|
| getMethylDiff |
Man page
|
| getMethylDiff,methylDiff-method |
Man page
|
| getMethylDiff,methylDiffDB-method |
Man page
|
| getMethylationStats |
Man page
|
| getMethylationStats,methylRaw-method |
Man page
|
| getMethylationStats,methylRawDB-method |
Man page
|
| getSampleID |
Man page
|
| getSampleID,methylBase-method |
Man page
|
| getSampleID,methylBaseDB-method |
Man page
|
| getSampleID,methylDiff-method |
Man page
|
| getSampleID,methylDiffDB-method |
Man page
|
| getSampleID,methylRaw-method |
Man page
|
| getSampleID,methylRawDB-method |
Man page
|
| getSampleID,methylRawList-method |
Man page
|
| getSampleID,methylRawListDB-method |
Man page
|
| getSampleID<- |
Man page
|
| getSampleID<-,methylBase-method |
Man page
|
| getSampleID<-,methylBaseDB-method |
Man page
|
| getSampleID<-,methylDiff-method |
Man page
|
| getSampleID<-,methylDiffDB-method |
Man page
|
| getSampleID<-,methylRaw-method |
Man page
|
| getSampleID<-,methylRawDB-method |
Man page
|
| getSampleID<-,methylRawList-method |
Man page
|
| getSampleID<-,methylRawListDB-method |
Man page
|
| getTabixByChr |
Source code
|
| getTabixByChunk |
Source code
|
| getTabixByOverlap |
Source code
|
| getTargetAnnotationStats |
Man page
Source code
|
| getTreatment |
Man page
|
| getTreatment,getTreatment,methylDiffDB-method |
Man page
|
| getTreatment,methylBase-method |
Man page
|
| getTreatment,methylBaseDB-method |
Man page
|
| getTreatment,methylDiff-method |
Man page
|
| getTreatment,methylDiffDB-method |
Man page
|
| getTreatment,methylRawList-method |
Man page
|
| getTreatment,methylRawListDB-method |
Man page
|
| getTreatment<- |
Man page
|
| getTreatment<-,methylBase-method |
Man page
|
| getTreatment<-,methylBaseDB-method |
Man page
|
| getTreatment<-,methylDiff-method |
Man page
|
| getTreatment<-,methylDiffDB-method |
Man page
|
| getTreatment<-,methylRawList-method |
Man page
|
| getTreatment<-,methylRawListDB-method |
Man page
|
| headTabix |
Source code
|
| influence |
Source code
|
| joinSegmentNeighbours |
Man page
Source code
|
| makeMethTabix |
Source code
|
| makeMethylBaseDB |
Source code
|
| makeMethylDB |
Man page
|
| makeMethylDB,methylBase-method |
Man page
|
| makeMethylDB,methylBase-methods |
Man page
|
| makeMethylDB,methylDiff-method |
Man page
|
| makeMethylDB,methylDiff-methods |
Man page
|
| makeMethylDB,methylRaw-method |
Man page
|
| makeMethylDB,methylRaw-methods |
Man page
|
| makeMethylDB,methylRawList-method |
Man page
|
| makeMethylDB,methylRawList-methods |
Man page
|
| makeMethylDiffDB |
Source code
|
| makeMethylRawDB |
Source code
|
| makeTabixHeader |
Source code
|
| mergeData.counts |
Source code
|
| mergeTabix |
Source code
|
| mergeTbxByChr |
Source code
|
| methCall |
Source code
|
| methRead |
Man page
|
| methRead,character,ANY,ANY-method |
Man page
|
| methRead,character,character,character-method |
Man page
|
| methRead,character-method |
Man page
|
| methRead,list,ANY,ANY-method |
Man page
|
| methRead,list,list,character-method |
Man page
|
| methSeg |
Man page
Source code
|
| methSeg2bed |
Man page
Source code
|
| methylBase |
Man page
|
| methylBase-class |
Man page
|
| methylBase.obj |
Man page
|
| methylBaseDB |
Man page
|
| methylBaseDB-class |
Man page
|
| methylDiff |
Man page
|
| methylDiff-class |
Man page
|
| methylDiff.obj |
Man page
|
| methylDiffDB |
Man page
|
| methylDiffDB-class |
Man page
|
| methylKit-defunct |
Man page
|
| methylRaw |
Man page
|
| methylRaw-class |
Man page
|
| methylRawDB |
Man page
|
| methylRawDB-class |
Man page
|
| methylRawList |
Man page
Source code
|
| methylRawList-class |
Man page
|
| methylRawList.obj |
Man page
|
| methylRawListDB |
Man page
Source code
|
| methylRawListDB-class |
Man page
|
| normalizeCoverage |
Man page
|
| normalizeCoverage,methylRawList-method |
Man page
|
| normalizeCoverage,methylRawListDB-method |
Man page
|
| obj2tabix |
Source code
|
| p.adjusted |
Source code
|
| percMethylation |
Man page
|
| percMethylation,methylBase-method |
Man page
|
| percMethylation,methylBaseDB-method |
Man page
|
| plotTargetAnnotation |
Man page
Source code
|
| pool |
Man page
|
| pool,methylBase-method |
Man page
|
| pool,methylBaseDB-method |
Man page
|
| processBismarkAln |
Man page
|
| processBismarkAln,character,character,character-method |
Man page
|
| processBismarkAln,list,list,character-method |
Man page
|
| read |
Man page
Source code
|
| read.bed |
Man page
Source code
|
| read.bismark |
Man page
Source code
|
| read.feature.flank |
Man page
Source code
|
| read.transcript.features |
Man page
Source code
|
| readMethylBaseDB |
Source code
|
| readMethylDB |
Man page
Source code
|
| readMethylDiffDB |
Source code
|
| readMethylRawDB |
Source code
|
| readTabixHeader |
Source code
|
| reconstruct |
Man page
|
| reconstruct,ANY,methylBase-method |
Man page
|
| reconstruct,ANY,methylBaseDB-method |
Man page
|
| reconstruct,methylBase-method |
Man page
|
| reconstruct,methylBaseDB-method |
Man page
|
| regionCounts |
Man page
|
| regionCounts,methylBase,GRanges-method |
Man page
|
| regionCounts,methylBase,GRangesList-method |
Man page
|
| regionCounts,methylBaseDB,GRanges-method |
Man page
|
| regionCounts,methylBaseDB,GRangesList-method |
Man page
|
| regionCounts,methylRaw,GRanges-method |
Man page
|
| regionCounts,methylRaw,GRangesList-method |
Man page
|
| regionCounts,methylRawDB,GRanges-method |
Man page
|
| regionCounts,methylRawDB,GRangesList-method |
Man page
|
| regionCounts,methylRawList,GRanges-method |
Man page
|
| regionCounts,methylRawList,GRangesList-method |
Man page
|
| regionCounts,methylRawListDB,GRanges-method |
Man page
|
| regionCounts,methylRawListDB,GRangesList-method |
Man page
|
| removeComp |
Man page
|
| removeComp,methylBase-method |
Man page
|
| removeComp,methylBaseDB-method |
Man page
|
| reorganize |
Man page
|
| reorganize,methylBase-method |
Man page
|
| reorganize,methylBaseDB-method |
Man page
|
| reorganize,methylRawList-method |
Man page
|
| reorganize,methylRawListDB-method |
Man page
|
| rowSds |
Source code
|
| select |
Man page
|
| select,methylBase-method |
Man page
|
| select,methylBaseDB-method |
Man page
|
| select,methylDiff-method |
Man page
|
| select,methylDiffDB-method |
Man page
|
| select,methylRaw-method |
Man page
|
| select,methylRawDB-method |
Man page
|
| selectByOverlap |
Man page
|
| selectByOverlap,methylBase,GRanges-method |
Man page
|
| selectByOverlap,methylBase-method |
Man page
|
| selectByOverlap,methylBaseDB,GRanges-method |
Man page
|
| selectByOverlap,methylBaseDB-method |
Man page
|
| selectByOverlap,methylDiff,GRanges-method |
Man page
|
| selectByOverlap,methylDiff-method |
Man page
|
| selectByOverlap,methylDiffDB,GRanges-method |
Man page
|
| selectByOverlap,methylDiffDB-method |
Man page
|
| selectByOverlap,methylRaw,GRanges-method |
Man page
|
| selectByOverlap,methylRaw-method |
Man page
|
| selectByOverlap,methylRawDB,GRanges-method |
Man page
|
| selectByOverlap,methylRawDB-method |
Man page
|
| selectByOverlap,methylRawList,GRanges-method |
Man page
|
| selectByOverlap,methylRawList-method |
Man page
|
| selectByOverlap,methylRawListDB,GRanges-method |
Man page
|
| selectByOverlap,methylRawListDB-method |
Man page
|
| show,methylBase |
Man page
|
| show,methylBase-method |
Man page
|
| show,methylBaseDB |
Man page
|
| show,methylBaseDB-method |
Man page
|
| show,methylDiff |
Man page
|
| show,methylDiff-method |
Man page
|
| show,methylDiffDB |
Man page
|
| show,methylDiffDB-method |
Man page
|
| show,methylRaw |
Man page
|
| show,methylRaw-method |
Man page
|
| show,methylRawDB |
Man page
|
| show,methylRawDB-method |
Man page
|
| show,methylRawList |
Man page
|
| show,methylRawList-method |
Man page
|
| show,methylRawListDB |
Man page
|
| show,methylRawListDB-method |
Man page
|
| sortPos |
Source code
|
| tabix2df |
Source code
|
| tabix2dt |
Source code
|
| tabix2gr |
Source code
|
| tileMethylCounts |
Man page
|
| tileMethylCounts,methylBase-method |
Man page
|
| tileMethylCounts,methylBaseDB-method |
Man page
|
| tileMethylCounts,methylRaw-method |
Man page
|
| tileMethylCounts,methylRawDB-method |
Man page
|
| tileMethylCounts,methylRawList-method |
Man page
|
| tileMethylCounts,methylRawListDB-method |
Man page
|
| unite |
Man page
|
| unite,methylRawList-method |
Man page
|
| unite,methylRawListDB-method |
Man page
|
| unite.methylRawList |
Source code
|
| updateMethObject |
Man page
|
| valid.methylBaseDB |
Source code
|
| valid.methylDiffDB |
Source code
|
| valid.methylRawDB |
Source code
|
| valid.methylRawListDB |
Source code
|
| valid.methylRawListObj |
Source code
|
| valid.methylRawObj |
Source code
|
| waldTest.DML |
Source code
|
| writeTabixHeader |
Source code
|
