casper
Characterization of Alternative Splicing based on Paired-End Reads

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283
Source code
31
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casper: Characterization of Alternative Splicing based on Paired-End Reads
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API for casper
Characterization of Alternative Splicing based on Paired-End Reads

Global functions
.assignRankings Source code
.buildRanks Source code
.checkExonRank Source code
.checkGeneIdAttrib Source code
.cleanSplicingsNAs Source code
.cleanTranscriptsNAs Source code
.deduceExonRankings Source code
.deduceTranscriptRangeData Source code
.deduceTranscriptsFromGTF Source code
.filterDrop Source code
.getUnusedColnames Source code
.massageZeroBasedRankings Source code
.mergeFramesViaRanges Source code
.prepareGFF3Fragments Source code
.prepareGFF3TXS Source code
.prepareGFF3Tables Source code
.prepareGFF3data.frame Source code
.prepareGFF3genes Source code
.prepareGFF3transcripts Source code
.prepareGFFMetadata Source code
.prepareGTFFragments Source code
.prepareGTFTables Source code
.prepareGTFdata.frame Source code
.prepareGTFgenes Source code
.prepareGTFtranscripts Source code
K562.r1l1 Man page
[,denovoGeneExpr,ANY,ANY,ANY-method Man page
[,denovoGenomeExpr,ANY,ANY,ANY-method Man page
[,modelPriorAS,ANY,ANY,ANY-method Man page
[,simulatedSamples,ANY,ANY,ANY-method Man page
[,simulatedSamples,missing,index,missing-method Man page
[[,denovoGeneExpr,ANY,ANY,ANY-method Man page
[[,denovoGeneExpr,ANY,ANY-method Man page
[[,denovoGenomeExpr,ANY,ANY-method Man page
[[,denovoGenomeExpr-method Man page
annotatedGenome Man page
annotatedGenome-class Man page
anovaAdjustment Source code
anovaAdjustment.ExpressionSet Source code
as.list,denovoGenomeExpr-method Man page
assignExons2GeneF Source code
asymmetryCheck Man page
asymmetryCheck,ExpressionSet-method Man page
asymmetryCheck,data.frame-method Man page
asymmetryCheck,matrix-method Man page
buildGene Source code
buildRD Source code
calcDenovo Man page Source code
calcDenovoMultiple Source code
calcExp Man page Source code
calcKnownMultiple Source code
casperDesign Man page Source code
casperSim Source code
coef,modelPriorAS,ANY,ANY,ANY-method Man page
coef,modelPriorAS-method Man page
coef,simulatedSamples-method Man page
constructDenovoGenomeObj Source code
createDenovoGenome Man page Source code
createGenome Source code
dbetabin Source code
deduceStrandSingleExonTx Source code
denovoExpr Man page Source code
denovoGeneExpr-class Man page
denovoGenomeExpr-class Man page
determineStrand Source code
dinvgammaVec Source code
distrsGSE37704 Man page
exprs,simulatedSamples-method Man page
findLongInserts Source code
findNewExonsF Source code
firstBamReads Source code
formatChromo Source code
formatDenovoOut Source code
genePlot Man page
genePlot,CompressedIRangesList,ANY,ANY,ANY,ANY-method Man page
genePlot,GRanges,ANY,ANY,ANY,ANY-method Man page
genePlot,GRangesList,ANY,ANY,ANY,ANY-method Man page
genePlot,IRanges,ANY,ANY,ANY,ANY-method Man page
genePlot,IRangesList,ANY,ANY,ANY,ANY-method Man page
genePlot,missing,character,annotatedGenome,GRanges,ExpressionSet Man page
genePlot,missing,character,annotatedGenome,missing,missing-metho Man page
genePlot,missing,character,annotatedGenome,procBam,ExpressionSet Man page
genePlot,missing,character,annotatedGenome,procBam,missing-metho Man page
genePlot-methods Man page
generateNOexons Source code
genomeBystrand Source code
getChr Man page
getChr,character,missing,missing,annotatedGenome-method Man page
getChr,missing,character,missing,annotatedGenome-method Man page
getChr,missing,missing,character,annotatedGenome-method Man page
getChr,missing,missing,missing,annotatedGenome-method Man page
getChr-method Man page
getDistrs Man page Source code
getDistrsAndPCs Source code
getDistrsFromBam Source code
getDistrsFrompBam Source code
getDistrsSplit Source code
getIsland Man page
getIsland,character,missing,annotatedGenome-method Man page
getIsland,missing,character,annotatedGenome-method Man page
getNBinomParams Source code
getNreads Man page
getNreads,pathCounts-method Man page
getReads Man page
getReads,procBam-method Man page
getRoc Man page
getRoc,logical,logical-method Man page
getRoc,matrix,matrix-method Man page
getRoc,numeric,numeric-method Man page
groups2int Source code
hg19DB Man page
lhoodGrid Source code
lines Man page
lines,readDistrs-method Man page
logrpkm Source code
logrpkm2thpi Source code
makeIslands Source code
matchCircularity Source code
matchTranscripts Man page Source code
mergeBatches Man page
mergeBatches,ExpressionSet,ExpressionSet-method Man page
mergeBatches,ExpressionSet,simulatedSamples-method Man page
mergeDisSub Source code
mergeDisWr Source code
mergeExp Man page Source code Source code
mergeGRanges Source code
mergeGenomeByChr Source code
mergePC Source code
mergePCWr Source code
mergePCs Source code Source code
mergePbam Source code
mergeStrDenovo Source code
modelPrior Man page Source code
modelPriorAS-class Man page
names,denovoGenomeExpr-method Man page
nbExonsDistrib Source code
nbReads Source code
nbVariantsDistrib Source code
pathCounts Man page
pathCounts,list-method Man page
pathCounts,procBam-method Man page
pathCounts-class Man page
pathCounts-method Man page
plot Man page
plot,readDistrs,ANY-method Man page
plot,readDistrsList,ANY-method Man page
plotExpr Man page
plotExpr,denovoGeneExpr-method Man page
plotExpr-methods Man page
plotPriorAS Man page
plotPriorAS,modelPriorAS-method Man page
plotPriorAS-methods Man page
posprob Man page
posprob,denovoGeneExpr-method Man page
probNonEquiv Man page
probNonEquiv,ExpressionSet-method Man page
probNonEquiv,list-method Man page
probNonMappable Source code
procB Source code
procBam Man page
procBam,ANY-method Man page
procBam,list,logical,integer,logical,character-method Man page
procBam,list,logical,integer,logical,missing-method Man page
procBam,list,logical,integer,missing,missing-method Man page
procBam,list,logical,missing,logical,missing-method Man page
procBam,list,logical,missing,missing,missing-method Man page
procBam,list,missing,integer,logical,missing-method Man page
procBam,list,missing,integer,missing,missing-method Man page
procBam,list,missing,missing,logical,missing-method Man page
procBam,list,missing,missing,missing,missing-method Man page
procBam,list,missing,numeric,missing,missing-method Man page
procBam-class Man page
procBam-method Man page
procBamF Source code
procGenome Man page
procGenome,GRanges,ANY-method Man page
procGenome,GRanges-method Man page
procGenome,TxDb,ANY-method Man page
procGenome,TxDb-method Man page
procPaths Source code
procsimPost Source code
pvalTreat Man page
pvalTreat,ExpressionSet-method Man page
pvalTreat,list-method Man page
qqgammaGenomeWide Man page
qqgammaGenomeWide,ExpressionSet-method Man page
qqgammaGenomeWide,data.frame-method Man page
qqgammaGenomeWide,matrix-method Man page
qqnormGenomeWide Man page
qqnormGenomeWide,ExpressionSet-method Man page
qqnormGenomeWide,data.frame-method Man page
qqnormGenomeWide,matrix-method Man page
quantileNorm Man page
quantileNorm,ExpressionSet-method Man page
quantileNorm,matrix-method Man page
relativeExpr Source code
relexprByGene Man page Source code
restoreUnknownStrand Source code
rgammatrunc Source code
rmDuplicateTxs Source code
rmShortInserts Man page Source code
rowSD Source code
rowVar Source code
rtruncexp Source code
show,annotatedGenome-method Man page
show,denovoGeneExpr-method Man page
show,denovoGenomeExpr-method Man page
show,modelPriorAS-method Man page
show,pathCounts-method Man page
show,procBam-method Man page
show,simulatedSamples-method Man page
simEstError Source code
simMAE Man page Source code
simMAEcheck Man page Source code
simMultSamples Man page Source code
simOneExp Source code
simPost Source code
simPostPred Source code
simReads Man page Source code
simnewsamplesGGcommonpar Source code
simnewsamplesNoisyObs Source code
simnewsamplesNoisyObs_old Source code
simulatedSamples-class Man page
splitGenomeByLength Man page Source code
splitPaths Source code
startDist Source code
subsetGenome Man page
subsetGenome,character,missing,annotatedGenome-method Man page
subsetGenome,missing,character,annotatedGenome-method Man page
subsetGenome-methods Man page
transDistr Source code
transcripts Man page
transcripts,annotatedGenome,character,missing-method Man page
transcripts,annotatedGenome,missing,character-method Man page
transcripts,annotatedGenome,missing,missing-method Man page
transferIslandid Source code
truncLenDis Source code
txLength Man page
txLength,character,missing,annotatedGenome-method Man page
txLength,missing,character,annotatedGenome-method Man page
txLength,missing,data.frame,annotatedGenome-method Man page
txLength,missing,missing,annotatedGenome-method Man page
txLength-methods Man page
txLengthBase Source code
uniquifyQname Source code
valid_annotatedGenome Source code
valid_denovoGeneExpr Source code
valid_denovoGenomeExpr Source code
valid_modelPriorAS Source code
valid_pathCounts Source code
valid_simulatedSamples Source code
variantMargExpr Source code
variants Man page
variants,denovoGeneExpr-method Man page
variants,denovoGenomeExpr-method Man page
variants<- Man page
variants<-,denovoGeneExpr-method Man page
wrapDenovo Man page Source code
wrapKnown Man page Source code
wrapKnownSingle Source code
wrapKnownStartFromPBam Source code
wrapKnownStartFromPBamSingle Source code
write.sam.header Source code
casper documentation built on Dec. 17, 2020, 2:01 a.m.

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