vd4mmind/methylkit
DNA methylation analysis from high-throughput bisulfite sequencing results

Package index
Search the vd4mmind/methylkit package
Vignettes
Functions
161
Source code
25
Man pages
51
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vd4mmind/methylkit: DNA methylation analysis from high-throughput bisulfite sequencing results
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API

API for vd4mmind/methylkit
DNA methylation analysis from high-throughput bisulfite sequencing results

Global functions
.CpG.dinuc.unify Source code
.adjlim Source code
.check.pipeline.list Source code
.cluster Source code
.dist.cor Source code
.nearest.2bed Source code
.pcaPlot Source code
.pcaPlotT Source code
.readTableFast Source code
.structureAMPoutput Source code
.structureGeneric Source code
PCASamples Man page
PCASamples,methylBase-method Man page
SLIMfunc Source code
[ Man page
[,methylBase-method Man page
[,methylDiff-method Man page
[,methylRaw-method Man page
adjust.methylC Man page
adjust.methylC,methylRaw,methylRaw-method Man page
adjust.methylC,methylRawList,methylRawList-method Man page
annotate.WithFeature Man page
annotate.WithFeature,GRanges,GRanges-method Man page
annotate.WithFeature,methylDiff,GRanges-method Man page
annotate.WithFeature.Flank Man page
annotate.WithFeature.Flank,GRanges,GRanges,GRanges-method Man page
annotate.WithFeature.Flank,methylDiff,GRanges,GRanges-method Man page
annotate.WithGenicParts Man page
annotate.WithGenicParts,GRanges,GRangesList-method Man page
annotate.WithGenicParts,methylDiff,GRangesList-method Man page
annotate.gr.WithGenicParts Source code
annotationByFeature Man page
annotationByFeature-class Man page
annotationByGenicParts Man page
annotationByGenicParts-class Man page
assocComp Man page Source code
bed12.to.exons Source code
bed12.to.introns Source code
bedgraph Man page
bedgraph,methylDiff-method Man page
bedgraph,methylRaw-method Man page
bedgraph,methylRawList-method Man page
calculateDiffMeth Man page
calculateDiffMeth,methylBase-method Man page
check.bed.validity Source code
clusterSamples Man page
clusterSamples,methylBase-method Man page
colSds Source code
diffMethPerChr Man page
diffMethPerChr,methylDiff-method Man page
distance2nearestFeature Source code
extract Man page
filterByCoverage Man page
filterByCoverage,methylRaw-method Man page
filterByCoverage,methylRawList-method Man page
get.methylDiff Man page
get.methylDiff,methylDiff-method Man page
getAssembly Man page
getAssembly,methylBase-method Man page
getAssembly,methylDiff-method Man page
getAssembly,methylRaw-method Man page
getAssociationWithTSS Man page
getAssociationWithTSS,annotationByGenicParts-method Man page
getContext Man page
getContext,methylBase-method Man page
getContext,methylDiff-method Man page
getContext,methylRaw-method Man page
getCorrelation Man page
getCorrelation,-methods Man page
getCorrelation,methylBase-method Man page
getCorrelation-method Man page
getCoverageStats Man page
getCoverageStats,methylRaw Man page
getCoverageStats,methylRaw-method Man page
getData Man page
getData,-methods Man page
getData,methylBase-method Man page
getData,methylDiff-method Man page
getData,methylRaw-method Man page
getData-method Man page
getFeatsWithTargetsStats Man page
getFeatsWithTargetsStats,annotationByFeature-method Man page
getFlanks Man page
getFlanks,GRanges-method Man page
getMembers Man page
getMembers,annotationByFeature-method Man page
getMethylationStats Man page
getMethylationStats,methylRaw-method Man page
getTargetAnnotationStats Man page
getTargetAnnotationStats,annotationByFeature-method Man page
merge2 Source code
methylBase Man page
methylBase-class Man page
methylBase.obj Man page
methylDiff Man page
methylDiff-class Man page
methylDiff.obj Man page
methylRaw Man page
methylRaw-class Man page
methylRawList Man page
methylRawList-class Man page
methylRawList.obj Man page
normalizeCoverage Man page
normalizeCoverage,methylRawList-method Man page
percMethylation Man page
percMethylation,methylBase-method Man page
plotTargetAnnotation Man page
plotTargetAnnotation,annotationByFeature-method Man page
pool Man page
pool,methylBase-method Man page
read Man page
read,character,character,character-method Man page
read,list,list,character-method Man page
read.bed Man page
read.bed,character-method Man page
read.bismark Man page
read.bismark,character,character,character-method Man page
read.bismark,list,list,character-method Man page
read.feature.flank Man page
read.feature.flank,character-method Man page
read.transcript.features Man page
read.transcript.features,character-method Man page
reconstruct Man page Source code
regionCounts Man page
regionCounts,methylBase,GRanges-method Man page
regionCounts,methylRaw,GRanges-method Man page
regionCounts,methylRaw,GRangesList-method Man page
regionCounts,methylRawList,GRanges-method Man page
regionCounts,methylRawList,GRangesList-method Man page
removeComp Man page Source code
reorganize Man page
reorganize,methylBase-method Man page
reorganize,methylRawList-method Man page
rowSds Source code
select Man page
select,methylBase-method Man page
select,methylDiff-method Man page
select,methylRaw-method Man page
show Man page
show,annotationByFeature-method Man page
show,annotationByGenicParts-method Man page
show,methylBase Man page
show,methylDiff Man page
show,methylRaw Man page
show,methylRawList Man page
tileMethylCounts Man page
tileMethylCounts,methylBase-method Man page
tileMethylCounts,methylRaw-method Man page
tileMethylCounts,methylRawList-method Man page
unite Man page
unite,-methods Man page
unite,methylRawList-method Man page
updateMethObject Man page
updateMethObject,methylBase-method Man page
updateMethObject,methylDiff-method Man page
updateMethObject,methylRaw-method Man page
updateMethObject,methylRawList-method Man page
valid.methylRawObj Source code
vd4mmind/methylkit documentation built on May 3, 2019, 4:57 p.m.

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