Files in charles-plessy/CAGEr
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

.Rbuildignore
.gitignore
CAGEr.github.Rproj
DESCRIPTION
NAMESPACE
NEWS
R/AggregationFunctions.R R/AggregationMethods.R R/AllClasses.R R/Annotations.R R/CAGEexp.R R/CAGEr.R R/CTSS.R R/ClusteringFunctions.R R/ClusteringMethods.R R/CorrelationMethods.R R/CumulativeDistributionFunctions.R R/CumulativeDistributionMethods.R R/ExportFunctions.R R/ExportMethods.R R/ExpressionProfilingMethods.R R/GetMethods.R R/ImportFunctions.R R/ImportMethods.R R/MergingMethods.R R/Multicore.R R/NormalizationFunctions.R R/NormalizationMethods.R R/QCmethods.R R/QuantileWidthFunctions.R R/QuantileWidthMethods.R R/Richness.R R/SetMethods.R R/ShiftingFunctions.R R/ShiftingMethods.R R/StrandInvaders.R benchmarks/sorted-abundance-benchmark.Rmd benchmarks/sorted-abundance-benchmark.md benchmarks/unique-signif.Rmd benchmarks/unique-signif.md
data/FANTOM5humanSamples.RData
data/FANTOM5mouseSamples.RData
data/exampleCAGEexp.RData
data/exampleCAGEset.RData
data/exampleZv9_annot.RData
inst/CITATION
inst/extdata/CAGEset.Rmd
inst/extdata/Zf.30p.dome.chr17.ctss
inst/extdata/Zf.high.chr17.ctss
inst/extdata/Zf.prim6.rep1.chr17.ctss
inst/extdata/Zf.prim6.rep2.chr17.ctss
inst/extdata/Zf.unfertilized.egg.chr17.ctss
inst/rmarkdown/templates/CAGEexp/skeleton/skeleton.Rmd
inst/rmarkdown/templates/CAGEexp/template.yaml
man/CAGEexp-class.Rd man/CAGEr-class.Rd man/CAGEr-package.Rd man/CAGEr_Multicore.Rd man/CAGEset-class.Rd man/CTSS-class.Rd man/CTSSclusteringMethod.Rd man/CTSScoordinates.Rd man/CTSScumulativesTagClusters.Rd man/CTSSnormalizedTpm.Rd man/CTSStagCount.Rd man/CTSStagCountTable.Rd man/CTSStoGenes.Rd man/CustomConsensusClusters.Rd man/FANTOM5humanSamples.Rd man/FANTOM5mouseSamples.Rd man/GeneExpDESeq2.Rd man/GeneExpSE.Rd man/QuantileWidthFunctions.Rd man/aggregateTagClusters.Rd man/annotateCTSS.Rd man/bam2CTSS.Rd man/byCtss.Rd man/clusterAggregateAndSum.Rd man/clusterCTSS.Rd man/coerceInBSgenome.Rd man/consensusClusterConvertors.Rd man/consensusClusters-set.Rd man/consensusClusters.Rd man/consensusClustersDESeq2.Rd man/consensusClustersQuantile.Rd man/consensusClustersTpm.Rd man/coverage-functions.Rd man/cumulativeCTSSdistribution.Rd man/distclu-functions.Rd man/exampleCAGEexp.Rd man/exampleCAGEset.Rd man/exampleZv9_annot.Rd man/exportCTSStoBedGraph.Rd man/exportToBed.Rd man/expressionClasses.Rd man/extractExpressionClass.Rd man/genomeName.Rd man/getCTSS.Rd man/getExpressionProfiles.Rd man/getShiftingPromoters.Rd man/hanabi-class.Rd man/hanabi.Rd man/hanabiPlot.Rd man/import.CAGEscanMolecule.Rd man/import.CTSS.Rd man/import.bam.Rd man/import.bam.ctss.Rd man/import.bedCTSS.Rd man/import.bedScore.Rd man/import.bedmolecule.Rd man/importPublicData.Rd man/inputFiles.Rd man/inputFilesType.Rd man/librarySizes.Rd man/loadFileIntoGPos.Rd man/mapStats.Rd man/mapStatsScopes.Rd man/mergeCAGEsets.Rd man/mergeSamples.Rd man/moleculesGR2CTSS.Rd man/normalizeTagCount.Rd man/parseCAGEscanBlocksToGrangeTSS.Rd man/plot.hanabi.Rd man/plotAnnot.Rd man/plotCorrelation.Rd man/plotExpressionProfiles.Rd man/plotInterquantileWidth.Rd man/plotReverseCumulatives.Rd man/powerLaw.Rd man/quantilePositions.Rd man/ranges2annot.Rd man/ranges2genes.Rd man/ranges2names.Rd man/sampleLabels.Rd man/scoreShift.Rd man/seqNameTotalsSE.Rd man/setColors.Rd man/show-methods.Rd man/strandInvaders.Rd man/summariseChrExpr.Rd man/tagClusterConvertors.Rd man/tagClusters.Rd man/tagClustersQuantile.Rd vignettes/CAGEexp.Rmd
vignettes/CAGEr.bib
vignettes/images/CAGEprotocol.svg
vignettes/images/CTSSbedGraph.svg
vignettes/images/ConsensusClustersBed.svg
vignettes/images/ConsensusClustersExpressionProfiles.svg
vignettes/images/CumulativeDistributionAndQuantiles.svg
vignettes/images/ShiftingPromoter.svg
vignettes/images/ShiftingScore.svg
vignettes/images/TagClustersBed.svg
charles-plessy/CAGEr documentation built on Aug. 29, 2018, 6:54 a.m.