Files in Repitools

Epigenomic tools

R/enrichmentCalc.R R/plotClusters.R R/findClusters.R R/maskOut.R R/checkProbes.R R/enrichmentPlot.R R/hyper.R R/getProbePositionsDf.R R/writeWig.R R/blocksStats.R R/GCbiasPlots.R R/empBayes.R R/abcdDNA.R R/summarizeScores.R R/utils.R R/annoDF2GR.R R/clusterPlots.R R/profilePlots.R R/relativeCN.R R/classes.R R/ChromaBlocks.R R/cpgBoxplots.R R/cpgDensityCalc.R R/featureScores.R R/annoGR2DF.R R/mergeReplicates.R R/chromosomeCNplots.R R/gcContentCalc.R R/processNimblegenArrays.R R/FastQC-class.R R/makeWindowLookup.R R/binPlots.R R/regionStats.R R/cpgDensityPlot.R R/sequenceCalc.R R/determineOffset.R R/methylEst.R R/GCadjustCopy.R R/annotationLookup.R R/mappabilityCalc.R R/multiHeatmap.R R/genomeBlocks.R R/genQC.R R/BAM2GRanges.R R/featureBlocks.R R/absoluteCN.R vignettes/qc-enrPlot.pdf vignettes/visualisations-binPlotsLine.pdf vignettes/visualisations-binPlotsHeatmap.pdf vignettes/qc-cpgPlot.pdf vignettes/visualisations-profPlots.pdf vignettes/visualisations-cluPlots3.pdf man/empBayes.Rd man/sequenceCalc.Rd man/maskOut.Rd man/GCAdjustParams-class.Rd man/chr21genes.Rd man/FastQC-class.Rd man/AffymetrixCdfFile-class.Rd man/binPlots.Rd man/ChromaResults-class.Rd man/methylEst.Rd man/AdjustedCopyEstimate-class.Rd man/checkProbes.Rd man/writeWig.Rd man/cpgDensityPlot.Rd man/annotationCounts.Rd man/multiHeatmap.Rd man/blocksStats.Rd man/BayMethList-class.Rd man/ScoresList-class.Rd man/annoDF2GR.Rd man/genomeBlocks.Rd man/chromosomeCNplots.Rd man/plotQdnaByCN.Rd man/gcContentCalc.Rd man/GCbiasPlots.Rd man/cpgDensityCalc.Rd man/regionStats.Rd man/MappabilitySource-class.Rd man/annotationLookup.Rd man/findClusters.Rd man/abcdDNA.Rd man/ChromaBlocks.Rd man/AffymetrixCelSet-class.Rd man/genQC.Rd man/featureScores.Rd man/annoGR2DF.Rd man/processNDF.Rd man/mergeReplicates.Rd man/determineOffset.Rd man/plotClusters.Rd man/relativeCN.Rd man/clusterPlots.Rd man/annotationBlocksCounts.Rd man/hcRegions.Rd man/loadPairFile.Rd man/QdnaData.Rd man/enrichmentPlot.Rd man/setCNVOffsets.Rd man/enrichmentCalc.Rd man/ClusteredScoresList-class.Rd man/summarizeScores.Rd man/cpgBoxPlots.Rd man/annotationBlocksLookup.Rd man/expr.Rd man/GCadjustCopy.Rd man/mappabilityCalc.Rd man/getSampleOffsets.Rd man/getProbePositionsDf.Rd man/loadSampleDirectory.Rd man/featureBlocks.Rd man/makeWindowLookupTable.Rd man/absoluteCN.Rd man/samplesList.Rd man/CopyEstimate-class.Rd man/BAM2GRanges.Rd man/hyper.Rd man/profilePlots.Rd tests/tests.R inst/doc/Repitools_vignette.pdf inst/doc/Repitools_vignette.R inst/examples/mergeReplicates_seq.R inst/examples/binPlots_seq.R inst/examples/clusterPlots_seq.R inst/examples/annotationCounts_seq.R inst/examples/enrichmentPlot_seq.R inst/examples/regionStats_affy.R inst/examples/blockStats_affy.R inst/examples/binPlots_affy.R inst/examples/findClusters_dataframe.R inst/examples/cpgDensityPlot_seq.R inst/examples/featureScores_array.R inst/examples/featureScores_seq.R