MalteThodberg/CAGEfightR
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

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Search the MalteThodberg/CAGEfightR package
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Functions
203
Source code
26
Man pages
55
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MalteThodberg/CAGEfightR: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
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API

API for MalteThodberg/CAGEfightR
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Global functions
.onLoad Source code
BC Source code
TCstats Source code
assignGeneID Man page
assignGeneID,GenomicRanges,GenomicRanges-method Man page
assignGeneID,GenomicRanges,TxDb-method Man page
assignGeneID,RangedSummarizedExperiment,GenomicRanges-method Man page
assignGeneID,RangedSummarizedExperiment,TxDb-method Man page
assignMissingID Man page
assignMissingID,GenomicRanges-method Man page
assignMissingID,RangedSummarizedExperiment-method Man page
assignMissingID,character-method Man page
assignTxID Man page
assignTxID,GenomicRanges,GenomicRanges-method Man page
assignTxID,GenomicRanges,TxDb-method Man page
assignTxID,RangedSummarizedExperiment,GenomicRanges-method Man page
assignTxID,RangedSummarizedExperiment,TxDb-method Man page
assignTxType Man page
assignTxType,GenomicRanges,GenomicRangesList-method Man page
assignTxType,GenomicRanges,TxDb-method Man page
assignTxType,RangedSummarizedExperiment,GenomicRangesList-method Man page
assignTxType,RangedSummarizedExperiment,TxDb-method Man page
asymmetricPercentiles Source code
balanceBC Man page Source code
balanceD Man page Source code
bam2bw Source code
bed2bg Source code
bed2bw Source code
bg2bw Source code
bg_mapper Source code
bw2bg Source code
bwCommonGenome Man page Source code
bwGenomeCompatibility Man page Source code
bwValid Man page
bwValid,BigWigFile-method Man page
bwValid,BigWigFileList-method Man page
bw_mapper Source code
bw_mapper2 Source code
bwg2bed Source code
calcBidirectionality Man page
calcBidirectionality,GPos-method Man page
calcBidirectionality,GRanges-method Man page
calcBidirectionality,RangedSummarizedExperiment-method Man page
calcComposition Man page Source code
calcPooled Man page Source code
calcShape Man page
calcShape,GRanges,GPos-method Man page
calcShape,GRanges,GRanges-method Man page
calcShape,GRanges,RangedSummarizedExperiment-method Man page
calcShape,RangedSummarizedExperiment,GRanges-method Man page
calcShape,RangedSummarizedExperiment,RangedSummarizedExperiment- Man page
calcSupport Man page Source code
calcTPM Man page Source code
calcTotalTags Man page Source code
checkCTSSs Man page
checkCTSSs,ANY-method Man page
checkCTSSs,BigWigFile-method Man page
checkCTSSs,GPos-method Man page
checkCTSSs,GRanges-method Man page
checkCTSSs,character-method Man page
checkGenomes Source code
checkPeaked Man page Source code
checkPooled Man page Source code
clusterBidirectionally Man page
clusterBidirectionally,GPos-method Man page
clusterBidirectionally,GRanges-method Man page
clusterBidirectionally,RangedSummarizedExperiment-method Man page
clusterUnidirectionally Man page
clusterUnidirectionally,GPos-method Man page
clusterUnidirectionally,GRanges-method Man page
clusterUnidirectionally,RangedSummarizedExperiment-method Man page
combineClusters Man page
combineClusters,RangedSummarizedExperiment,RangedSummarizedExper Man page
convertBAM2BigWig Man page Source code
convertBED2BedGraph Man page Source code
convertBED2BigWig Man page Source code
convertBedGraph2BED Man page Source code
convertBedGraph2BigWig Man page Source code
convertBigWig2BED Man page Source code
convertBigWig2BedGraph Man page Source code
convertGRanges2GPos Man page Source code
corHelper Source code
countClusters Source code
countScoredOverlaps Source code
coverageWindows Source code
determineOrientation Source code
exampleBidirectional Man page
exampleCTSSs Man page
exampleDesign Man page
exampleGenes Man page
exampleUnidirectional Man page
extendRanges Source code
findBidirRegions Source code
findLinks Man page
findLinks,GRanges-method Man page
findLinks,RangedSummarizedExperiment-method Man page
findStretches Man page
findStretches,GRanges-method Man page
findStretches,RangedSummarizedExperiment-method Man page
gf_mapper Source code
gf_reducer Source code
gf_reducer2 Source code
gf_wrapper Source code
gf_wrapper2 Source code
isobreak Source code
padlag Source code
quantifyCTSSs Man page
quantifyCTSSs,BigWigFileList,BigWigFileList-method Man page
quantifyCTSSs,character,character-method Man page
quantifyCTSSs2 Man page Source code
quantifyClusters Man page Source code
quantifyGenes Man page Source code
quickEnhancers Man page Source code
quickGenes Man page Source code
quickTSSs Man page Source code
shapeEntropy Man page Source code
shapeIQR Man page Source code
shapeMean Man page Source code
shapeMultimodality Man page Source code
splitByStrand Source code
splitPooled Source code
subsetByBidirectionality Man page
subsetByBidirectionality,GPos-method Man page
subsetByBidirectionality,GRanges-method Man page
subsetByBidirectionality,RangedSummarizedExperiment-method Man page
subsetByComposition Man page Source code
subsetBySupport Man page Source code
summarizeWidths Source code
swapRanges Man page
swapRanges,GenomicRanges-method Man page
swapRanges,RangedSummarizedExperiment-method Man page
swapScores Man page Source code
symmetricPercentiles Source code
trackBalance Man page
trackBalance,GPos-method Man page
trackBalance,GRanges-method Man page
trackBalance,RangedSummarizedExperiment-method Man page
trackCTSS Man page
trackCTSS,GPos-method Man page
trackCTSS,GRanges-method Man page
trackCTSS,RangedSummarizedExperiment-method Man page
trackClusters Man page
trackClusters,GRanges-method Man page
trackClusters,RangedSummarizedExperiment-method Man page
trackLinks Man page Source code
trimToPeak Man page
trimToPeak,GRanges,GPos-method Man page
trimToPeak,GRanges,GRanges-method Man page
trimToPeak,GRanges,RangedSummarizedExperiment-method Man page
trimToPeak,RangedSummarizedExperiment,GenomicRanges-method Man page
trimToPeak,RangedSummarizedExperiment,RangedSummarizedExperiment Man page
trimToPercentiles Man page
trimToPercentiles,GRanges,GPos-method Man page
trimToPercentiles,GRanges,GRanges-method Man page
trimToPercentiles,GRanges,RangedSummarizedExperiment-method Man page
trimToPercentiles,RangedSummarizedExperiment,GenomicRanges-metho Man page
trimToPercentiles,RangedSummarizedExperiment,RangedSummarizedExp Man page
tuneTagClustering Man page
tuneTagClustering,GPos-method Man page
tuneTagClustering,GRanges-method Man page
tuneTagClustering,RangedSummarizedExperiment-method Man page
utilsAggregateRows Man page
utilsAggregateRows,dgCMatrix-method Man page
utilsAggregateRows,matrix-method Man page
utilsDeStrand Man page Source code
utilsScoreOverlaps Man page Source code
utilsSimplifyTxDb Man page Source code
MalteThodberg/CAGEfightR documentation built on Sept. 11, 2021, 4:42 a.m.

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