API for mctp/codac
Comprehensive Detection and Analysis of Chimeras

Global functions
addCyto Source code
addExpressionGeneLoci Source code
addExpressionSJ Source code
addNames Source code
alignBreakpoints Source code
alignContigs Source code
alignWrapper Source code
alignment.stat Source code
assembleBreakpoint Source code
assembleBreakpoints Source code
assembleChain 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
extractChimeric Source code
filterBundle Source code
filterTS Source code
filterTranscripts 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
makeTranscripts Source code
mergeJNC Source code
motifBreakpoints Source code
naTo0 Source code
naToBlank Source code
omitBlank Source code
orientJunctions Source code
parseSVs Source code
positionChains Source code
prepareTxs 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
report Source code
reportMini Source code
reportSV Source code
runGmap Source code
runInchworm Source code
runMinimap2 Source code
slBundle Source code
slFormat Source code
slReport Source code
splice.rate Source code
splitBundle Source code
statBundle Source code
statPlot Source code
stitchChain Source code
stitchChains 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
mctp/codac documentation built on Nov. 9, 2017, 3:22 p.m.