API for MPIIComputationalEpigenetics/epiRepeatR
epiRepeatR

Global functions
GenomeAlignment Source code
GenomeMethylationCalls Source code
GenomeRepeatTrack Source code
RepeatAlignment Source code
RepeatAlignmentBiSeq Source code
RepeatAlignmentChip Source code
RepeatEpigenomeCollection Man page Source code
RepeatEpigenomeCollection-class Man page
RepeatReference Source code
RepeatTree Source code
addFile Source code
addLeafs Source code
adjustAttr.midpoint Source code
assembleRepeatsInCuratedFamilyTree Source code
bitwCompl Source code
colorize.value Source code
convertPhredCharToInt Source code
countAllReads.bam Source code
countMappedReads.bam Source code
countMappedReads.bam.perSeq Source code
countUnmappedReads.bam Source code
createLinearTree Source code
createRepPlot_groupSummaryTrees_meth Source code
createRepPlot_markTree Source code
createStump Source code
dendrogramAttributeCombineRecursive Source code
dendrogramMergeSimple Source code
expandReadSeqFromCigar Source code
expandRefSeqFromCigar Source code
explainSamFlags Source code
filterRepRefChip Man page
filterRepRefChip,RepeatEpigenomeCollection-method Man page
filterRepRefMeth Man page
filterRepRefMeth,RepeatEpigenomeCollection-method Man page
getAlnStats Source code
getAnnot Man page
getAnnot,RepeatEpigenomeCollection-method Man page
getArgParser Man page Source code
getCharVecHeadString Source code
getConfigElement Man page Source code
getCuratedRepeatFamilyTree Source code
getDNAStringForReference Source code
getFgColorForBg Source code
getFileTypeFromFileName Source code
getFlagStats Source code
getMarks Man page
getMarks,RepeatEpigenomeCollection-method Man page
getMatchStr Source code
getMemberAttr Source code
getReadStatsFromSample Source code
getReferenceInfo Source code
getRepRef Man page
getRepRef,RepeatEpigenomeCollection-method Man page
getRepeatCovg Man page
getRepeatCovg,RepeatEpigenomeCollection-method Man page
getRepeatFromEmbl Source code
getRepeatMaskerTable Source code
getRepeatScores Man page
getRepeatScores,RepeatEpigenomeCollection-method Man page
getSampleGroups Man page Source code
getSampleMarkTable Man page
getSampleMarkTable,RepeatEpigenomeCollection-method Man page
getSamples Man page
getSamples,RepeatEpigenomeCollection-method Man page
getScanBamFilterFlags Source code
getTaxOrder Source code
indexRepeatReference.bowtie2 Source code
indexRepeatReference.bwa Source code
inferMarkTypes Source code
isCpgAtPosMethInRead Source code
isLeaf Source code
list2dend Source code
loadConfig Man page Source code
loadConfigFromCommandLine Man page Source code
logger.cmd.args Man page Source code
mergeMethGr Source code
normalizeMatrix Man page Source code
parseEMBL Source code
parseMcTable.bissnp Source code
plotDend.rec Source code
plotHeatmap Source code
plotRepeatAlignmentStats Man page Source code
printAln Source code
readFileTable Source code
repPlot_groupSummary Source code
runAnalysis Man page Source code
saveConfig Man page Source code
setConfigElement Man page Source code
setMemberAttr Source code
setUpParallelFromConfig Source code
simplifyRepeatFamilies Source code
treefork Source code
MPIIComputationalEpigenetics/epiRepeatR documentation built on May 10, 2017, 4:04 a.m.