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

NEWS.md R/AggregationMethods.R R/Annotations.R R/CAGEexp.R R/CAGEfightR.R R/CAGEr-package.R R/CAGEr.R R/CTSS.R R/ClusteringFunctions.R R/ClusteringMethods.R R/CorrelationMethods.R R/CumulativeDistributionMethods.R R/Distclu.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/Paraclu.R R/QCmethods.R R/QuantileWidthMethods.R R/ResetMethods.R R/Richness.R R/RleDataFrame.R R/SetMethods.R R/ShiftingFunctions.R R/ShiftingMethods.R R/StrandInvaders.R R/TSSlogo.R benchmarks/BED12-blockInfo-benchmark.Rmd benchmarks/BED12-blockInfo-benchmark.md benchmarks/cumulative_sums.Rmd benchmarks/cumulative_sums.md benchmarks/dominant_ctss.Rmd benchmarks/dominant_ctss.md benchmarks/paraclcu.Rmd benchmarks/paraclcu.md benchmarks/quantile_position.Rmd benchmarks/quantile_position.md benchmarks/rowSums_on_Rle_DF.Rmd benchmarks/rowSums_on_Rle_DF.md benchmarks/rowsum_on_Rle_DF.Rmd benchmarks/rowsum_on_Rle_DF.md benchmarks/sorted-abundance-benchmark.Rmd benchmarks/sorted-abundance-benchmark.md benchmarks/unique-signif.Rmd benchmarks/unique-signif.md inst/rmarkdown/templates/CAGEexp/skeleton/skeleton.Rmd man/CAGEexp-class.Rd man/CAGEr-class.Rd man/CAGEr-package.Rd man/CAGEr_Multicore.Rd man/CTSS-class.Rd man/CTSScoordinates.Rd man/CTSScumulativesTagClusters.Rd man/CTSSnormalizedTpm.Rd man/CTSStagCount.Rd man/CTSStoGenes.Rd man/ConsensusClusters-class.Rd man/CustomConsensusClusters.Rd man/FANTOM5humanSamples.Rd man/FANTOM5mouseSamples.Rd man/GeneExpDESeq2.Rd man/GeneExpSE.Rd man/QuantileWidthFunctions.Rd man/TSSlogo.Rd man/TagClusters-class.Rd man/aggregateTagClusters.Rd man/annotateCTSS.Rd man/bam2CTSS.Rd man/byCtss.Rd man/coerceInBSgenome.Rd man/consensusClusters-set.Rd man/consensusClusters.Rd man/consensusClustersDESeq2.Rd man/consensusClustersQuantile.Rd man/consensusClustersTpm.Rd man/cumulativeCTSSdistribution.Rd man/distclu.Rd man/dot-ctss_summary_for_clusters.Rd man/exampleCAGEexp.Rd man/exampleZv9_annot.Rd man/exportToTrack.Rd man/expressionClasses.Rd man/filteredCTSSidx.Rd man/flagByUpstreamSequences.Rd man/flagLowExpCTSS.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/paraclu.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/quickEnhancers.Rd man/ranges2annot.Rd man/ranges2genes.Rd man/ranges2names.Rd man/resetCAGEexp.Rd man/rowSums.RleDataFrame.Rd man/rowsum.RleDataFrame.Rd man/sampleLabels.Rd man/scoreShift.Rd man/seqNameTotalsSE.Rd man/setColors.Rd man/strandInvaders.Rd man/summariseChrExpr.Rd man/tagClusters.Rd vignettes/CAGE_Resources.Rmd vignettes/CAGEexp.Rmd