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 |
computeDiffMat.counts.deseq2 | 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_differential | 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 |
filterRepRefAcc | Man page |
filterRepRefAcc,RepeatEpigenomeCollection-method | Man page |
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 |
getComparisonInfo | Man page |
getComparisonInfo,RepeatEpigenomeCollection-method | Man page |
getComparisons | Man page |
getComparisons,RepeatEpigenomeCollection-method | Man page |
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 |
getRepeatScoresDiff | Man page |
getRepeatScoresDiff,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 |
makeBinary | Source code |
mergeMethGr | Source code |
normalizeMatrix | Man page Source code |
parseEMBL | Source code |
parseMcTable.bissnp | Source code |
parseMcTable.epp | Source code |
plotDend.rec | Source code |
plotHeatmap | Source code |
plotRepeatAlignmentStats | Man page Source code |
printAln | Source code |
rankDESeqTab | Source code |
readFileTable | Source code |
repPlot_differential | 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 |
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