Files in ataudt/aneufinder

Analysis of Copy Number Variation in Single-Cell-Sequencing Data

R/Aneufinder.R R/aneufinder-package.R R/bedimport.R R/binReads.R R/blacklist.R R/checkUserInput.R R/clusterHMMs.R R/collapseBins.R R/compareMethods.R R/consensusSegments.R R/correctionMethods.R R/dnbinom.R R/documented_objects.R R/export.R R/findCNVs.R R/findSCEs.R R/getBreakpoints.R R/getDistinctColors.R R/global.R R/gtools.R R/hotspotter.R R/importReads.R R/initializeStates.R R/karyotypeMeasures.R R/loadFromFiles.R R/makeBins.R R/plotting.R R/printMethods.R R/qualityMeasures.R R/rwConfig.R R/simulateReads.R R/startup.R R/subsetByCNVprofile.R R/timedMessage.R R/zinbinom.R README.md man/AneuFinder-package.Rd man/Aneufinder.Rd man/DNAcopy.findCNVs.Rd man/HMM.findCNVs.Rd man/aneuBiHMM.Rd man/aneuHMM.Rd man/annotateBreakpoints.Rd man/bam2GRanges.Rd man/bed2GRanges.Rd man/bi.edivisive.findCNVs.Rd man/biDNAcopy.findCNVs.Rd man/biHMM.findCNVs.Rd man/binReads.Rd man/binned.data.Rd man/binning.Rd man/blacklist.Rd man/clusterByQuality.Rd man/clusterHMMs.Rd man/collapseBins.Rd man/colors.Rd man/compareMethods.Rd man/compareModels.Rd man/consensusSegments.Rd man/correctGC.Rd man/edivisive.findCNVs.Rd man/estimateComplexity.Rd man/export.Rd man/filterSegments.Rd man/findCNVs.Rd man/findCNVs.strandseq.Rd man/findHotspots.Rd man/fixedWidthBins.Rd man/getBreakpoints.Rd man/getDistinctColors.Rd man/getQC.Rd man/getSCEcoordinates.Rd man/heatmapAneuploidies.Rd man/heatmapGenomewide.Rd man/heatmapGenomewideClusters.Rd man/hotspotter.Rd man/hotspotter.variable.Rd man/importBed.Rd man/initializeStates.Rd man/karyotypeMeasures.Rd man/loadFromFiles.Rd man/mergeStrandseqFiles.Rd man/plot.GRanges.Rd man/plot.GRangesList.Rd man/plot.aneuBiHMM.Rd man/plot.aneuHMM.Rd man/plot.character.Rd man/plotHeterogeneity.Rd man/plotHistogram.Rd man/plotKaryogram.Rd man/plotProfile.Rd man/plot_pca.Rd man/print.aneuBiHMM.Rd man/print.aneuHMM.Rd man/qualityControl.Rd man/readConfig.Rd man/refineBreakpoints.Rd man/simulateReads.Rd man/subsetByCNVprofile.Rd man/transCoord.Rd man/variableWidthBins.Rd man/writeConfig.Rd man/zinbinom.Rd tests/testthat.R tests/testthat/test_convergence.R