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 |
| 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 |
