Comprehensive Detection and Analysis of Chimeras

Global functions | |
---|---|

addCyto | Source code |

addExpressionGeneLoci | Source code |

addExpressionSJ | Source code |

addNames | Source code |

alignBreakpoints | Source code |

alignContigsToTranscripts | Source code |

alignWrapperBreakpoint | Source code |

alignWrapperChain | Source code |

alignment.stat | Source code |

alignmentsToBreakpoints | Source code |

assemble | Source code |

assembleBreakpoint | Source code |

assembleBreakpoints | Source code |

assembleChimeras | Source code |

assembleFusions | Source code |

associateBreakpoints | Source code |

breakpoint.stat | Source code |

breakpointValidate | Source code |

bsBundle | Source code |

bsFormat | Source code |

bsReport | Source code |

chainBreakpoints | Source code |

chimeric.sig | Source code |

classifyBreakpoints | Source code |

collapseBreakpoints | Source code Source code |

config | Source code |

coverage.tbl | Source code |

defineBreakpointArtifacts | Source code |

defineHCbreakpoints | Source code |

defineHIbreakpoints | Source code |

defineHQbreakpoints | Source code |

defineHQjunctions | Source code |

defineHRbreakpoints | Source code |

defineHXBreakpoints | Source code |

defineLevels | Source code |

detect | Source code |

distanceBreakpoints | Source code |

dustJunctions | Source code |

dustySplit | Source code |

filterBundle | Source code |

filterContigTranscripts | Source code |

fixRanges | Source code |

getBam | Source code |

getREC | Source code |

importBundles | Source code |

l2g | Source code |

l2g.full | Source code |

lgt | Source code |

linkBreakpoints | Source code |

locus.stat | Source code |

makeAnnotations | Source code |

makeBundle | Source code |

makeCoreAnnotations | Source code |

makeDirectory | Source code |

makeFeatures | Source code |

makeFrames | Source code |

makeGenes | Source code |

makeMaskAnnotations | Source code |

makeMiscAnnotations | Source code |

makeOverlapAnnotations | Source code |

makeParams | Source code |

makeStat | Source code |

makeTranscripts | Source code |

mergeBundles | Source code |

mergeJNC | Source code |

motifBreakpoints | Source code |

naTo0 | Source code |

naToBlank | Source code |

neo.report | Source code |

neoFormat | Source code |

neoReport | Source code |

omitBlank | Source code |

orientJunctions | Source code |

pairAlignmentBreakpoints | Source code |

parseSVs | Source code |

positionAlignments | Source code |

qc.report | Source code |

qcFormat | Source code |

readBam | Source code |

readCounts | Source code |

readFormat | Source code |

readJunctions | Source code |

readREC | Source code |

readSEQ | Source code |

readSJ | Source code |

readSplices | Source code |

readTAG | Source code |

realignContigs | Source code |

report | Source code |

reportMini | Source code |

reportSV | Source code |

runDetect | Source code |

runGmap | Source code |

runInchworm | Source code |

runMinimap2 | Source code |

sewBreakpoints | Source code |

sewContigs | Source code |

slBundle | Source code |

slFormat | Source code |

slReport | Source code |

splice.rate | Source code |

splitBundle | Source code |

statPlot | Source code |

svBundle | Source code |

svChainCircos | Source code |

svFormat | Source code |

svReport | Source code |

svSig | Source code |

svSigPlot | Source code |

topologyBreakpoints | Source code |

tsBundle | Source code |

tsFormat | Source code |

tsReport | Source code |

validateBreakpoints | Source code |

writeFastas | Source code |

writePairFastas | Source code |

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