Files in CAGEr
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
NEWS
NAMESPACE
DESCRIPTION
R/CumulativeDistributionMethods.R
R/AggregationMethods.R
R/QCmethods.R
R/ImportFunctions.R
R/CAGEr.R
R/Richness.R
R/AggregationFunctions.R
R/StrandInvaders.R
R/MergingMethods.R
R/Annotations.R
R/AllClasses.R
R/ClusteringMethods.R
R/QuantileWidthFunctions.R
R/ExportFunctions.R
R/Multicore.R
R/ExpressionProfilingMethods.R
R/ShiftingFunctions.R
R/CumulativeDistributionFunctions.R
R/ClusteringFunctions.R
R/NormalizationFunctions.R
R/GetMethods.R
R/ImportMethods.R
R/ExportMethods.R
R/CAGEexp.R
R/QuantileWidthMethods.R
R/SetMethods.R
R/NormalizationMethods.R
R/ShiftingMethods.R
R/CTSS.R
R/CorrelationMethods.R
inst/CITATION
inst/doc/CAGE_Resources.Rmd
inst/doc/CAGE_Resources.html
inst/doc/CAGE_Resources.R
inst/doc/CAGEexp.html
inst/doc/CAGEexp.R
inst/doc/CAGEexp.Rmd
inst/rmarkdown/templates/CAGEexp/template.yaml
inst/rmarkdown/templates/CAGEexp/skeleton/skeleton.Rmd
inst/extdata/Zf.prim6.rep2.chr17.ctss
inst/extdata/Zf.high.chr17.ctss
inst/extdata/CAGEset.Rmd
inst/extdata/Zf.prim6.rep1.chr17.ctss
inst/extdata/Zf.30p.dome.chr17.ctss
inst/extdata/Zf.unfertilized.egg.chr17.ctss
build/vignette.rds
vignettes/CAGE_Resources.Rmd
vignettes/CAGEr.bib
vignettes/CAGEexp.Rmd
vignettes/images/TagClustersBed.svg
vignettes/images/ShiftingScore.svg
vignettes/images/ConsensusClustersExpressionProfiles.svg
vignettes/images/CAGEprotocol.svg
vignettes/images/CumulativeDistributionAndQuantiles.svg
vignettes/images/ConsensusClustersBed.svg
vignettes/images/CTSSbedGraph.svg
vignettes/images/ShiftingPromoter.svg
data/exampleZv9_annot.RData
data/FANTOM5humanSamples.RData
data/FANTOM5mouseSamples.RData
data/exampleCAGEset.RData
data/exampleCAGEexp.RData
man/CAGEr-package.Rd
man/consensusClustersDESeq2.Rd
man/consensusClustersTpm.Rd
man/consensusClusters-set.Rd
man/tagClusterConvertors.Rd
man/CTSStoGenes.Rd
man/clusterCTSS.Rd
man/import.bedmolecule.Rd
man/seqNameTotalsSE.Rd
man/import.bam.Rd
man/tagClustersQuantile.Rd
man/getCTSS.Rd
man/normalizeTagCount.Rd
man/GeneExpSE.Rd
man/exportToBed.Rd
man/import.bedScore.Rd
man/byCtss.Rd
man/CAGEexp-class.Rd
man/plot.hanabi.Rd
man/aggregateTagClusters.Rd
man/inputFilesType.Rd
man/moleculesGR2CTSS.Rd
man/exampleCAGEexp.Rd
man/ranges2names.Rd
man/import.CAGEscanMolecule.Rd
man/import.bam.ctss.Rd
man/scoreShift.Rd
man/genomeName.Rd
man/hanabiPlot.Rd
man/plotCorrelation.Rd
man/powerLaw.Rd
man/parseCAGEscanBlocksToGrangeTSS.Rd
man/clusterAggregateAndSum.Rd
man/CustomConsensusClusters.Rd
man/ranges2annot.Rd
man/CAGEr_Multicore.Rd
man/hanabi-class.Rd
man/annotateCTSS.Rd
man/distclu-functions.Rd
man/getExpressionProfiles.Rd
man/CTSScoordinates.Rd
man/quantilePositions.Rd
man/CTSStagCount.Rd
man/summariseChrExpr.Rd
man/coverage-functions.Rd
man/CTSS-class.Rd
man/librarySizes.Rd
man/exportCTSStoBedGraph.Rd
man/tagClusters.Rd
man/consensusClustersQuantile.Rd
man/mapStatsScopes.Rd
man/mergeCAGEsets.Rd
man/ranges2genes.Rd
man/FANTOM5mouseSamples.Rd
man/import.CTSS.Rd
man/hanabi.Rd
man/coerceInBSgenome.Rd
man/sampleLabels.Rd
man/strandInvaders.Rd
man/consensusClusterConvertors.Rd
man/cumulativeCTSSdistribution.Rd
man/importPublicData.Rd
man/CTSSnormalizedTpm.Rd
man/CAGEr-class.Rd
man/mergeSamples.Rd
man/expressionClasses.Rd
man/FANTOM5humanSamples.Rd
man/CTSStagCountTable.Rd
man/consensusClusters.Rd
man/plotAnnot.Rd
man/CTSScumulativesTagClusters.Rd
man/QuantileWidthFunctions.Rd
man/import.bedCTSS.Rd
man/plotExpressionProfiles.Rd
man/mapStats.Rd
man/GeneExpDESeq2.Rd
man/exampleZv9_annot.Rd
man/setColors.Rd
man/CTSSclusteringMethod.Rd
man/extractExpressionClass.Rd
man/inputFiles.Rd
man/plotInterquantileWidth.Rd
man/CAGEset-class.Rd
man/getShiftingPromoters.Rd
man/bam2CTSS.Rd
man/show-methods.Rd
man/exampleCAGEset.Rd
man/plotReverseCumulatives.Rd
man/loadFileIntoGPos.Rd
