c-mertes/FraseR
Find RAre Splicing Events in RNA-Seq Data

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Search the c-mertes/FraseR package
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Functions
364
Source code
44
Man pages
25
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c-mertes/FraseR: Find RAre Splicing Events in RNA-Seq Data
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API

API for c-mertes/FraseR
Find RAre Splicing Events in RNA-Seq Data

Global functions
.onLoad Source code
.setPseudoCount Source code
D Source code
E Source code
FRASER Man page Source code
FRASER.mcols.get Man page Source code
FRASER.mcols.replace Source code
FRASER.results Source code
FRASER.rowRanges.get Man page Source code
FRASER.rowRanges.replace Source code
FUN Source code
FraserDataSet Man page Source code
FraserDataSet-class Man page
FraserDataSet.assays.replace_pre Source code
FraserDataSet.assays.replace_r36 Source code
FraserDataSet.assays.replace_r40 Source code
FraserDataSet.assays.set_r36 Source code
FraserDataSet.assays.set_r40 Source code
GRanges2SAF Source code
H Source code
K Man page Source code
N Man page Source code
[,FraserDataSet,ANY,ANY,ANY-method Man page
`D<-` Source code
`E<-` Source code
`addToAvailableFDRsubsets<-` Source code
`availableFDRsubsets<-` Source code
`b<-` Source code
`currentNoiseAlpha<-` Source code
`currentType<-` Source code
`dontWriteHDF5<-` Source code
`featureExclusionMask<-` Man page Source code
`fitMetrics<-` Source code
`hyperParams<-` Source code
`noise<-` Source code
`pVals<-` Source code
`padjVals<-` Source code
`predictedMeans<-` Source code
`rho<-` Source code
`setAssayMatrix<-` Source code
`zScores<-` Source code
aberrant,FraserDataSet-method Man page
aberrant.FRASER Source code
addCountsToFraserDataSet Man page Source code
addHRef Source code
adjust_FWER_PValues Source code
annotateIntronReferenceOverlap Man page Source code
annotatePotentialImpact Man page
annotateRanges Man page Source code
annotateRangesWithTxDb Man page Source code
annotateSpliceSite Source code
applyExpressionFilters Source code
applyExpressionFilters_jaccard Source code
applyVariabilityFilters Source code
applyVariabilityFilters_jaccard Source code
asFDS Source code
asSE Source code
assayExists Source code
assayNames,FraserDataSet-method Man page
assays,FraserDataSet-method Man page
assays<-,FraserDataSet,DelayedMatrix-method Man page
assays<-,FraserDataSet,SimpleList-method Man page
assays<-,FraserDataSet,list-method Man page
availableFDRsubsets Man page Source code
b Source code
bamFile Man page
bamFile,FraserDataSet-method Man page
bamFile<- Man page
bamFile<-,FraserDataSet-method Man page
bestNoise Source code
bestQ Man page Source code
betabinVglmTest Source code
calculatePSIValuePrimeSite Source code
calculatePSIValues Man page Source code
calculatePadjValues Man page
calculatePadjValuesOnSubset Man page
calculatePvalues Man page Source code
calculateZscore Man page Source code
checkCountData Source code
checkForAndCreateDir Source code
checkFraserDataSet Source code
checkNaAndRange Source code
checkPadjAvailableForFilters Source code
checkReadType Source code
checkSeqLevelStyle Source code
cleanCache Source code
collapseResTablePerGene Source code
condition Man page
condition,FraserDataSet-method Man page
condition<- Man page
condition<-,FraserDataSet-method Man page
countNonSplicedReads Man page Source code
countRNA Man page
countRNAData Man page Source code
countSplitReads Man page Source code
countSplitReadsPerChromosome Source code
counts,FraserDataSet-method Man page
counts<-,FraserDataSet,ANY-method Man page
createFullLinkTable Source code
createTestFraserDataSet Man page Source code
createTestFraserSettings Man page Source code
currentNoiseAlpha Source code
currentType Man page Source code
currentType<- Man page
deltaPsiValue Man page Source code
dontWriteHDF5 Man page Source code
dontWriteHDF5<- Man page
estLgammaAlpha Source code
estLgammaBeta Source code
estRho Source code
eval_prot Source code
extractChromosomeLengths Source code
extractChromosomes Source code
extractSpliceSiteCoordinates Source code
extractSpliceSiteCoordsPerStrand Source code
fds-methods Man page
featureExclusionMask Man page Source code
featureExclusionMask, Man page
featureExclusionMask<- Man page
filterExpression,FraserDataSet-method Man page
filterExpression.FRASER Source code
filterExpression.FRASER2 Source code
filterExpressionAndVariability Man page Source code
filterExpression_jaccard Source code
filterVariability Man page
filterVariability,FraserDataSet-method Man page
filterVariability.FRASER Source code
filterVariability.FRASER2 Source code
filterVariability_jaccard Source code
filtering Man page
findEncodingDim Source code
findJunctionsForAberrantGenes Source code
fit Man page
fit.FraserDataSet Man page Source code
fitAutoencoder Source code
fitBB Source code
fitFraserAE Source code
fitMetrics Man page Source code
fitMetrics<- Man page
fitPCA Source code
fit_autoenc Source code
flagBlacklistRegions Man page
fraserQQplotPlotly Source code
fullNLL Source code
fullNLLRho_penalized Source code
getAbsMaxByGroup Source code
getAssayAsVector Source code
getAssayMatrix Source code
getBPParam Source code
getEncDimRange Source code
getEnsemblBrowser Source code
getEnsemblSymbolLink Source code
getExACLink Source code
getFraserHDF5File Source code
getGeneCardsLink Source code
getGenomAD Source code
getGoogleLink Source code
getHDF5ChunkSize Source code
getHGNCLink Source code
getHyperOptimCorrectionMethod Source code
getMaxChunks2Read Source code
getNonSplicedCountCacheFile Source code
getNonSplicedCountCacheFolder Source code
getNonSplitReadCountsForAllSamples Man page Source code
getOmimLink Source code
getSamplesByChunk Source code
getSplitCountCacheFile Source code
getSplitReadCountsForAllSamples Man page Source code
getStrandString Source code
getSubsetVector Source code
getTrueDeltaPsi Source code
getTrueOutliers Source code
getter_setter_functions Man page
hyperParams Man page Source code
initAutoencoder Source code
injectOutliers Man page Source code
length,FraserDataSet-method Man page
limitGeneNamesList Source code
loadFraserDataSet Man page Source code
log2fc Source code
logger Source code
lossED Source code
makeSimulatedFraserDataSet Man page Source code
makeSimulatedFraserDataSet_BetaBinomial Source code
makeSimulatedFraserDataSet_Multinomial Source code
mapSeqlevels Man page Source code
mergeBamParams Source code
mergeCounts Man page Source code
mergeExternalData Man page Source code
methodOfMomentsRho Source code
na2default Source code
na2false Source code
na2zero Source code
name Man page
name,FraserDataSet-method Man page
name<- Man page
name<-,FraserDataSet-method Man page
nameNoSpace Source code
needsHyperOpt Source code
negLogLikelihoodRho Source code
noise Source code
nonSplicedReads Man page
nonSplicedReads,FraserDataSet-method Man page
nonSplicedReads<- Man page
nonSplicedReads<-,FraserDataSet-method Man page
null2default Source code
null2na Source code
optimHyperParams Man page Source code
pVals Man page Source code
pVals, Man page
padjVals Man page Source code
padjVals, Man page
pairedEnd Man page
pairedEnd,FraserDataSet-method Man page
pairedEnd<- Man page
pairedEnd<-,FraserDataSet-method Man page
pasteTable Source code
plotAberrantPerSample Man page
plotAberrantPerSample,FraserDataSet-method Man page
plotBamCoverage Man page
plotBamCoverageFromResultTable Man page
plotBasePlot Source code
plotCountCorHeatmap Man page
plotCountCorHeatmap,FraserDataSet-method Man page
plotEncDimSearch Man page
plotEncDimSearch,FraserDataSet-method Man page
plotExpectedVsObservedPsi Man page
plotExpression Man page
plotFilterExpression Man page
plotFilterVariability Man page
plotFunctions Man page
plotManhattan Man page
plotManhattan,FraserDataSet-method Man page
plotQQ Man page
plotQQ,FraserDataSet-method Man page
plotSpliceMetricRank Man page
plotVolcano Man page
plotVolcano,FraserDataSet-method Man page
plotVolcano.FRASER Source code
potentialImpactAnnotations Man page
predictMu Source code
predictMuCpp Source code
predictY Source code
predictYCpp Source code
predict_outliers Source code
predictedMeans Man page Source code
pseudocount Man page Source code
psiTypes Man page
putCounts2Memory Source code
pvalueByBetaBinomialPerType Source code
readJunctionMap Source code
removeInjectedOutliers Source code
restoreInjectedOutliers Source code
results,FraserDataSet-method Man page
resultsSingleSample Source code
rho Man page Source code
rho, Man page
samples Man page
samples,FraserDataSet-method Man page
samples<- Man page
samples<-,FraserDataSet-method Man page
saveAsHDF5 Source code
saveFraserDataSet Man page Source code
saveSpliceSiteCoordinates Source code
scanBamParam Man page
scanBamParam,FraserDataSet-method Man page
scanBamParam<- Man page
scanBamParam<-,FraserDataSet-method Man page
showFraserDataSet Source code
singleDFit Source code
splitGenes Source code
strandSpecific Man page
strandSpecific,FraserDataSet-method Man page
strandSpecific<- Man page
strandSpecific<-,FraserDataSet-method Man page
subset.FRASER Man page Source code
subsetKMostVariableJunctions Source code
table2character Source code
truncGrad_db Source code
truncGrad_e Source code
truncNLL_db Source code
truncNLL_e Source code
truncNLL_rho Source code
truncNLL_rho_penalized Source code
truncWeightedGrad_db Source code
truncWeightedNLL_db Source code
trunc_negLogLikelihoodRho Source code
trunc_negLogLikelihoodRho_penalized Source code
tryCatchFactory Source code
uniformSeqInfo Source code
uniqueIgnoreNA Source code
updateD Source code
updateE Source code
updateLossList Source code
updateRho Source code
validateAssays Source code
validateBamParam Source code
validateFraserDataSet Source code
validateName Source code
validateNonSplicedReadsSanity Source code
validateNonSplicedReadsType Source code
validatePairedEnd Source code
validateSampleAnnotation Source code
validateStrandSpecific Source code
validateWorkingDir Source code
variableJunctions Source code
verbose Man page
verbose<- Man page
vglmInfos2character Source code
whichPSIType Source code
whichReadType Source code
workingDir Man page
workingDir,FraserDataSet-method Man page
workingDir<- Man page
workingDir<-,FraserDataSet-method Man page
x Source code
zScore, Man page
zScores Man page Source code
c-mertes/FraseR documentation built on June 15, 2024, 3:29 a.m.

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