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
.github/.gitignore
.github/workflows/check-bioc.yml
.gitignore
CAGEr.github.Rproj
DESCRIPTION
NAMESPACE
NEWS.md
R/AggregationMethods.R
R/Annotations.R
R/CAGEexp.R
R/CAGEfightR.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/QuantileWidthMethods.R
R/ResetMethods.R
R/Richness.R
R/RleDataFrame.R
R/SetMethods.R
R/ShiftingFunctions.R
R/ShiftingMethods.R
R/StrandInvaders.R
benchmarks/BED12-blockInfo-benchmark.Rmd
benchmarks/BED12-blockInfo-benchmark.md
benchmarks/cumulative_sums.Rmd
benchmarks/cumulative_sums.html
benchmarks/cumulative_sums.md
benchmarks/cumulative_sums_files/figure-html/benchmark-1.png
benchmarks/dominant_ctss.Rmd
benchmarks/dominant_ctss.md
benchmarks/dominant_ctss_files/figure-html/unnamed-chunk-3-1.png
benchmarks/paraclcu.Rmd
benchmarks/paraclcu.html
benchmarks/paraclcu.md
benchmarks/paraclcu_files/figure-html/benchmarks-1.png
benchmarks/quantile_position.Rmd
benchmarks/quantile_position.md
benchmarks/quantile_position_files/figure-html/benchmark-1.png
benchmarks/rowSums_on_Rle_DF.Rmd
benchmarks/rowSums_on_Rle_DF.md
benchmarks/rowSums_on_Rle_DF_files/figure-html/benchmark-1.png
benchmarks/rowsum_on_Rle_DF.Rmd
benchmarks/rowsum_on_Rle_DF.md
benchmarks/rowsum_on_Rle_DF_files/figure-html/benchmark-1.png
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/exampleZv9_annot.RData
inst/CITATION
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/CTSS-class.Rd
man/CTSSclusteringMethod.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/TagClusters-class.Rd
man/aggregateTagClusters.Rd
man/annotateCTSS.Rd
man/bam2CTSS.Rd
man/byCtss.Rd
man/clusterCTSS.Rd
man/coerceInBSgenome.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/exampleZv9_annot.Rd
man/exportToTrack.Rd
man/expressionClasses.Rd
man/flagByUpstreamSequences.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/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/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
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
