API for JunctionSeq
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data

Global functions
DESeq2.gt.1.14 Source code
DEUresultTable Source code
JS.arrowChars Source code
JS.axis Source code
JS.perGeneQValue Source code
JS.perGeneQValueBySimulation Source code
JS.perGeneQValueExact Source code
JUNCTIONSEQ.DEFAULT.COLOR.LIST Man page
JunctionSeqCountSet Man page
JunctionSeqCountSet-class Man page
JunctionSeqHTML Source code
adapted.estimateDispersionsFit Source code
adapted.estimateDispersionsMAP Source code
adapted.estimateDispersionsPriorVar Source code
adapted.localDispersionFit Source code
adapted.parametricDispersionFit Source code
add.gene.name.annotation Source code
advlines Source code
apply2 Source code
applyByDimname Source code
applyByDimnameOLD Source code
arrangeCoefs Source code
balanceFeatures Source code
build.log.scale Source code
buildAllPlots Man page Source code
buildAllPlotsForGene Man page Source code
calc.filtered.adjusted.p Source code
color2transparent Source code
color2transparentVector Source code
constructModelFrame Source code
convertHeightToWidth Source code
convertWidthToHeight Source code
countTableForGene Source code
countbinIDs Source code
defaultColorList Man page
device.limits Source code
doesArrayContainDim Source code
drawGene Source code
drawGene.noSplices Source code
drawHalfLoop Source code
drawHalfLoops Source code
drawPlot Source code
drawTranscript Source code
estimateEffectSizes Man page Source code
estimateEffectSizes.BigModel Source code
estimateFeatureDispersionFromRow Source code
estimateJunctionSeqDispersions Man page Source code
estimateJunctionSeqSizeFactors Man page Source code
estimateSizeFactors Source code
estimateSizeFactorsForMatrix Source code
estimateUnsharedDispersions Source code
estimatelog2FoldChanges Source code
extractFromArray Source code
extractPlottingEstimates_helper Source code
f.na Source code
fit.character.vector Source code
fit.character.vector.helper Source code
fit.title Source code
fit.vert Source code
fitAndArrangeCoefs Source code
fitBeta Source code
fitBetaWrapper Source code
fitDisp Source code
fitDispGrid Source code
fitDispGridWrapper Source code
fitDispWrapper Source code
fitDispersionFunction Source code
fitDispersionFunctionHelper_SIMPLE Source code
fitDispersionFunction_advancedMode Source code
fitDispersionFunction_simpleMode Source code
fitJunctionSeqDispersionFunction Man page Source code
fixRHEL5_svg_bug Source code
formatArray Source code
geneCountTable Source code
geneIDs Source code
generate.interval.scale Source code
generateAllExpressionEstimates Source code
generateAllExpressionEstimates.v2 Source code
get.character.dim Source code
get.connection.cramp Source code
get.expression.data Source code
get.filtered.padjust Source code
get.nested.heights Source code
get.nested.heights.FALLBACK Source code
get.nested.heights.advanced Source code
get.nested.heights.depths Source code
get.nested.heights.helper Source code
get.norcounts.data Source code
get.rawcounts.data Source code
get.rexpr.data Source code
get.sig.genes Source code
getAllData Source code
getAllData2 Source code
getAllDataList Source code
getAllJunctionSeqCountVectors Source code
getAutofitTxRelativeHeight Source code
getBPParam Source code
getColCt Source code
getEffectsForPlotting Source code
getLogFoldChangeFromModel Source code
getModelFit Source code
getMyApply Source code
getPlottingDeviceFileExtension Source code
getPlottingDeviceFunc Source code
getPredictedEstimates Source code
getPredictedEstimatesGeneLevel Source code
getTimeAndDiff Source code
junctionSeqColors Man page
loadAndCleanJSCS Source code
logConditionalLikelihood Source code
make.evenly.spaced.seq Source code
make.evenly.spaced.seq.minor Source code
make.progress.report.fcn Source code
makeAllPlotPages Source code
makeAnalysisNavTable Source code
makeDESeqDataSetFromJSCS Source code
makeGeneLevelAxis Source code
makeGeneNavTable Source code
makeGeneWiseTable Source code
makeNavTable Source code
makePlotPage Source code
makeStyleKeyTable Source code
makeTablePage Source code
makevstaxis Source code
mapGeneNames Source code
mapGeneNamesToList Source code
modelFrameForGene Source code
modelFrameForGene.v2 Source code
newJunctionSeqCountSet Source code
overmerge.list Source code
plotDispEsts Man page Source code
plotJunctionSeqResultsForGene Man page Source code
plotMA Man page Source code
plotMA.OLDVER Source code
plotMA_HELPER Source code
plotTranscriptsOnly Source code
plotting.limits Source code
qorts.axis.break Source code
readAnnotationData Man page Source code
readGeneInfo Source code
readJunctionSeqCounts Man page Source code
repString Source code
reportMem Source code
reportTimeAndDiff Source code
rescale.coords Source code
rmDepCols Source code
runJunctionSeqAnalyses Man page Source code
shrink.character.vector Source code
shrink.character.vector.VERT Source code
simpleDeparse Source code
simpleReportMem Source code
strStartsWith Source code
strheightSRT90 Source code
subsetByGenes Source code
testFeatureForDJU.fromCountVector Source code
testFeatureForDJU.fromRow Source code
testFeatureForDJU.fromRow.simpleNormDist Source code
testForDiffUsage Man page Source code
testForDiffUsage.simpleNormDist Source code
timediff Source code
timestamp Source code
truncateAggregateGene Source code
vst Source code
write.fmt.table Source code
write.junction.bed.file Source code
write.junction.bed.file.GTFCONVERT Source code
write.simple.table.gz Source code
write.table.gz Source code
writeCompleteResults Man page Source code
writeExprBedTrack Man page Source code
writeSigBedTrack Man page Source code
writeSizeFactors Man page Source code
JunctionSeq documentation built on May 31, 2017, 3:24 p.m.