CAGEr
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Package index
Search the CAGEr package
Vignettes
Functions
389
Source code
32
Man pages
89
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CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
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API

API for CAGEr
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Global functions
.add.alpha Source code
.applyThreshold Source code
.byCtss Man page
.byCtss,data.table-method Man page
.checkqLowUp Source code
.cluster.ctss.chr Man page
.cluster.ctss.chr.predef Source code
.cluster.ctss.strand Man page
.cluster.ctss.strand.predef Source code
.clusterAggregateAndSum Man page
.clusterAggregateAndSum,GRanges-method Man page
.clusterAggregateAndSum,data.frame-method Man page
.clusterAggregateAndSum,data.table-method Man page
.clusterExpression Source code
.ctss2clusters Man page
.ctss2clusters.predef Source code
.distclu Man page
.estimate.G.addition.and.correct Source code
.export.bedgraph Source code
.export.bedgraph.all Source code
.export.bw.all Source code
.extract.cluster.info Source code
.fit.power.law.to.reverse.cumulative Source code
.get.dominant.ctss Source code
.get.quant.pos Man page Source code
.getCAGEsignalCoverage Man page
.getCumsum Man page
.getCumsumChr2 Man page
.hanabi Man page
.ksPvalue Source code
.ksStat Source code
.make.cluster.bed.track Source code
.myColorMatrix Source code
.normalize.to.reference.power.law.distribution Source code
.normalizeTagCount_switcher Source code
.pKS2 Source code
.paraclu Source code
.paraclu1 Source code
.paraclu2 Source code
.paraclu3 Source code
.pkstwo Source code
.plot.clusters.beanplots Source code
.plotCorrelation2 Source code
.plotReverseCumulative Source code
.powerLaw Man page
.predefined.clusters Source code
.remove.added.G Source code
.remove.added.G.CTSS Source code
.reverse.cumsum Source code
.score.promoter.shifting Source code
.summarize.clusters Man page
.summarize.clusters.predef Source code
.uncumsum Source code
CAGEexp Man page
CAGEexp-class Man page
CAGEr Man page
CAGEr-class Man page
CAGEr-package Man page
CAGEr_Multicore Man page
CAGEset Man page
CAGEset-class Man page
CCdataframe2granges Man page Source code
CCgranges2dataframe Man page Source code
CTSS Man page
CTSS-class Man page
CTSS.chr-class Man page
CTSSclusteringMethod Man page
CTSSclusteringMethod,CAGEexp-method Man page
CTSSclusteringMethod,CAGEset-method Man page
CTSSclusteringMethod,GRangesList-method Man page
CTSSclusteringMethod<- Man page
CTSSclusteringMethod<-,CAGEexp-method Man page
CTSSclusteringMethod<-,CAGEset-method Man page
CTSSclusteringMethod<-,GRangesList-method Man page
CTSScoordinates Man page
CTSScoordinates,CAGEexp-method Man page
CTSScoordinates,CAGEset-method Man page
CTSScoordinatesGR Man page
CTSScoordinatesGR,CAGEexp-method Man page
CTSScoordinatesGR,CAGEset-method Man page
CTSScoordinatesGR<- Man page
CTSScoordinatesGR<-,CAGEexp-method Man page
CTSScoordinatesGR<-,CAGEset-method Man page
CTSScumulativesCC Man page
CTSScumulativesCC,CAGEexp-method Man page
CTSScumulativesCC,CAGEset-method Man page
CTSScumulativesTagClusters Man page
CTSScumulativesTagClusters,CAGEexp-method Man page
CTSScumulativesTagClusters,CAGEset-method Man page
CTSScumulativesTagClusters<- Man page
CTSScumulativesTagClusters<-,CAGEexp-method Man page
CTSScumulativesTagClusters<-,CAGEset-method Man page
CTSSnormalizedTpm Man page
CTSSnormalizedTpm,CAGEexp-method Man page
CTSSnormalizedTpm,CAGEset-method Man page
CTSSnormalizedTpmDF Man page
CTSSnormalizedTpmDF,CAGEexp-method Man page
CTSSnormalizedTpmDF,CAGEset-method Man page
CTSSnormalizedTpmDf Man page
CTSSnormalizedTpmDf,CAGEexp-method Man page
CTSSnormalizedTpmDf,CAGEset-method Man page
CTSSnormalizedTpmGR Man page
CTSSnormalizedTpmGR,CAGEr-method Man page
CTSStagCount Man page
CTSStagCount,CAGEexp-method Man page
CTSStagCount,CAGEset-method Man page
CTSStagCountDA Man page
CTSStagCountDA,CAGEr-method Man page
CTSStagCountDF Man page
CTSStagCountDF,CAGEexp-method Man page
CTSStagCountDF,CAGEset-method Man page
CTSStagCountDf Man page
CTSStagCountDf,CAGEexp-method Man page
CTSStagCountDf,CAGEset-method Man page
CTSStagCountGR Man page
CTSStagCountGR,CAGEr-method Man page
CTSStagCountSE Man page
CTSStagCountSE,CAGEexp-method Man page
CTSStagCountSE,CAGEset-method Man page
CTSStagCountSE<- Man page
CTSStagCountSE<-,CAGEexp-method Man page
CTSStagCountSE<-,CAGEset-method Man page
CTSStagCountTable Man page
CTSStagCountTable,CAGEexp-method Man page
CTSStagCountTable,CAGEset-method Man page
CTSStoGenes Man page
CTSStoGenes,CAGEexp-method Man page
CTSStoGenes,CAGEset-method Man page
CustomConsensusClusters Man page
CustomConsensusClusters,CAGEexp,GRanges-method Man page
FANTOM5humanSamples Man page
FANTOM5mouseSamples Man page
GeneExpDESeq2 Man page
GeneExpDESeq2,CAGEexp-method Man page
GeneExpDESeq2,CAGEset-method Man page
GeneExpSE Man page
GeneExpSE,CAGEexp-method Man page
GeneExpSE,CAGEset-method Man page
Strand invaders Man page
TCdataframe2granges Man page Source code
TCgranges2dataframe Man page Source code
addCTSScolumn Source code
aggregateTagClusters Man page
aggregateTagClusters,CAGEr-method Man page
annotateCTSS Man page
annotateCTSS,CAGEexp,GRanges-method Man page
annotateCTSS,CAGEset,ANY-method Man page
annotateConsensusClusters Man page
annotateConsensusClusters,CAGEexp,GRanges-method Man page
annotateConsensusClusters,CAGEset,ANY-method Man page
bam2CTSS Man page Source code
checkFilesExist Source code
checkMergeOK Source code
clusterCTSS Man page
clusterCTSS,CAGEexp-method Man page
clusterCTSS,CAGEset-method Man page
coerce,CTSS,GRanges-method Man page
coerce,GRanges,CTSS-method Man page
coerce,data.frame,CAGEexp-method Man page
coerce,data.frame,CAGEset-method Man page
coerceInBSgenome Man page Source code
consensusClusterConvertors Man page
consensusClusters Man page
consensusClusters,CAGEr-method Man page
consensusClusters<- Man page
consensusClusters<-,CAGEexp-method Man page
consensusClusters<-,CAGEset-method Man page
consensusClustersDESeq2 Man page
consensusClustersDESeq2,CAGEexp-method Man page
consensusClustersDESeq2,CAGEset-method Man page
consensusClustersGR Man page
consensusClustersGR,CAGEexp-method Man page
consensusClustersGR,CAGEset-method Man page
consensusClustersGR<- Man page
consensusClustersGR<-,CAGEexp-method Man page
consensusClustersGR<-,CAGEset-method Man page
consensusClustersQuantile Man page
consensusClustersQuantile,CAGEexp-method Man page
consensusClustersQuantile,CAGEset-method Man page
consensusClustersQuantileLow Man page
consensusClustersQuantileLow,CAGEexp-method Man page
consensusClustersQuantileLow,CAGEset-method Man page
consensusClustersQuantileLow<- Man page
consensusClustersQuantileLow<-,CAGEset-method Man page
consensusClustersQuantileUp Man page
consensusClustersQuantileUp,CAGEexp-method Man page
consensusClustersQuantileUp,CAGEset-method Man page
consensusClustersQuantileUp<- Man page
consensusClustersQuantileUp<-,CAGEset-method Man page
consensusClustersSE Man page
consensusClustersSE,CAGEexp-method Man page
consensusClustersSE,CAGEset-method Man page
consensusClustersSE<- Man page
consensusClustersSE<-,CAGEexp,RangedSummarizedExperiment-method Man page
consensusClustersSE<-,CAGEset,ANY-method Man page
consensusClustersTpm Man page
consensusClustersTpm,CAGEexp-method Man page
consensusClustersTpm,CAGEset-method Man page
corVector Source code
coverage-functions Man page
cumulativeCTSSdistribution Man page
cumulativeCTSSdistribution,CAGEr-method Man page
distclu-functions Man page
exampleCAGEexp Man page
exampleCAGEset Man page
exampleZv9_annot Man page
exportCTSStoBedGraph Man page
exportCTSStoBedGraph,CAGEr-method Man page
exportToBed Man page
exportToBed,CAGEr-method Man page
expressionClasses Man page
expressionClasses,CAGEexp-method Man page
expressionClasses,CAGEset-method Man page
extractExpressionClass Man page
extractExpressionClass,CAGEexp-method Man page
extractExpressionClass,CAGEset-method Man page
findStrandInvaders Man page
findStrandInvaders,CAGEexp-method Man page
findStrandInvaders,CTSS-method Man page
genomeName Man page
genomeName,CAGEexp-method Man page
genomeName,CAGEset-method Man page
genomeName,CTSS-method Man page
genomeName<- Man page
genomeName<-,CAGEexp-method Man page
genomeName<-,CAGEset-method Man page
genomeName<-,CTSS-method Man page
getCTSS Man page
getCTSS,CAGEexp-method Man page
getCTSS,CAGEset-method Man page
getExpressionProfiles Man page
getExpressionProfiles,CAGEset-method Man page
getRefGenome Source code
getShiftingPromoters Man page
getShiftingPromoters,CAGEset-method Man page
hanabi Man page
hanabi,GRanges-method Man page
hanabi,List-method Man page
hanabi,Rle-method Man page
hanabi,integer-method Man page
hanabi,list-method Man page
hanabi,matrix-method Man page
hanabi,numeric-method Man page
hanabi-class Man page
hanabiPlot Man page
import.CAGEscanMolecule Man page Source code
import.CTSS Man page Source code
import.bam Man page Source code
import.bam.ctss Man page Source code
import.bedCTSS Man page Source code
import.bedScore Man page Source code
import.bedmolecule Man page Source code
importPublicData Man page
importPublicData,character,character,ANY,character-method Man page
initialize,CTSS-method Man page
inputFiles Man page
inputFiles,CAGEexp-method Man page
inputFiles,CAGEset-method Man page
inputFiles<- Man page
inputFiles<-,CAGEexp-method Man page
inputFiles<-,CAGEset-method Man page
inputFilesType Man page
inputFilesType,CAGEexp-method Man page
inputFilesType,CAGEset-method Man page
inputFilesType<- Man page
inputFilesType<-,CAGEexp-method Man page
inputFilesType<-,CAGEset-method Man page
librarySizes Man page
librarySizes,CAGEexp-method Man page
librarySizes,CAGEset-method Man page
lines.hanabi Man page Source code
loadFileIntoGPos Man page Source code
mapStats Man page Source code
mapStatsScopes Man page
mergeCAGEsets Man page
mergeCAGEsets,CAGEexp,CAGEexp-method Man page
mergeCAGEsets,CAGEset,CAGEset-method Man page
mergeSamples Man page
mergeSamples,CAGEexp,ANY-method Man page
mergeSamples,CAGEset,numeric-method Man page
moleculesGR2CTSS Man page Source code
msScope_all Man page
msScope_annotation Man page
msScope_counts Man page
msScope_mapped Man page
msScope_qc Man page
msScope_steps Man page
myRowSumsL Source code
normalizeTagCount Man page
normalizeTagCount,CAGEexp-method Man page
normalizeTagCount,CAGEset-method Man page
parseCAGEscanBlocksToGrangeTSS Man page
plot.hanabi Man page Source code
plotAnnot Man page
plotAnnot,CAGEexp-method Man page
plotAnnot,DataFrame-method Man page
plotAnnot,data.frame-method Man page
plotCorrelation Man page
plotCorrelation,CAGEr-method Man page
plotCorrelation2 Man page
plotCorrelation2,CAGEexp-method Man page
plotCorrelation2,CAGEset-method Man page
plotCorrelation2,DataFrame-method Man page
plotCorrelation2,SummarizedExperiment-method Man page
plotCorrelation2,data.frame-method Man page
plotCorrelation2,matrix-method Man page
plotExpressionProfiles Man page
plotExpressionProfiles,CAGEset-method Man page
plotInterquantileWidth Man page
plotInterquantileWidth,CAGEr-method Man page
plotReverseCumulatives Man page
plotReverseCumulatives,CAGEr-method Man page
points.hanabi Man page Source code
quantilePositions Man page
quantilePositions,CAGEr-method Man page
ranges2annot Man page
ranges2genes Man page
ranges2names Man page
removeStrandInvaders Man page
removeStrandInvaders,CAGEexp-method Man page
removeStrandInvaders,CTSS-method Man page
sampleLabels Man page
sampleLabels,CAGEexp-method Man page
sampleLabels,CAGEset-method Man page
sampleLabels,CTSS-method Man page
sampleLabels<- Man page
sampleLabels<-,CAGEexp-method Man page
sampleLabels<-,CAGEset-method Man page
sampleLabels<-,CTSS-method Man page
sampleList Man page
sampleList,CAGEr-method Man page
scoreShift Man page
scoreShift,CAGEset-method Man page
se2grPlusOrMinus Source code
seqNameTotalsSE Man page
seqNameTotalsSE,CAGEexp-method Man page
seqNameTotalsSE,CAGEset-method Man page
seqNameTotalsSE<- Man page
setColors Man page
setColors,CAGEr-method Man page
show,CAGEset-method Man page
show-methods Man page
summariseChrExpr Man page
summariseChrExpr,CAGEexp-method Man page
tagClusterConvertors Man page
tagClusters Man page
tagClusters,CAGEr-method Man page
tagClustersGR Man page
tagClustersGR,CAGEexp-method Man page
tagClustersGR,CAGEset-method Man page
tagClustersGR<- Man page
tagClustersGR<-,CAGEexp,ANY,TagClusters-method Man page
tagClustersGR<-,CAGEexp,missing,GRangesList-method Man page
tagClustersGR<-,CAGEset,ANY,ANY-method Man page
tagClustersQuantile Man page
tagClustersQuantile,CAGEexp-method Man page
tagClustersQuantile,TagClusters-method Man page
tagClustersQuantileLow Man page
tagClustersQuantileLow,CAGEexp-method Man page
tagClustersQuantileLow,CAGEset-method Man page
tagClustersQuantileLow<- Man page
tagClustersQuantileLow<-,CAGEexp-method Man page
tagClustersQuantileLow<-,CAGEset-method Man page
tagClustersQuantileUp Man page
tagClustersQuantileUp,CAGEexp-method Man page
tagClustersQuantileUp,CAGEset-method Man page
tagClustersQuantileUp<- Man page
tagClustersQuantileUp<-,CAGEset-method Man page
toCTSSdt Source code
CAGEr documentation built on Jan. 17, 2021, 2 a.m.

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