Files in chromstaR

Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

README.md R/scanBinsizes.R R/makeBins.R R/estimate.RAM.consumption.R R/frequencyAnalysis.R R/stateBrewer.R R/expressionAnalysis.R R/exportFiles.R R/zinbinom.R R/Chromstar.R R/checkUserInput.R R/callPeaksReplicates.R R/subsample.R R/combineMultivariates.R R/export.R R/mergeChroms.R R/readCustomBedFile.R R/testit.R R/peak_manipulation.R R/getCombinations.R R/changePostCutoff.R R/loadHmmsFromFiles.R R/startup.R R/getDistinctColors.R R/chromstaR-package.R R/simulate.R R/removeCondition.R R/rwConfig.R R/plotting.R R/stateorderByTransition.R R/collapseBins.R R/documented_objects.R R/segmentation.R R/dec2bin.R R/importReads.R R/printMethods.R R/documented_plotting.R R/callPeaksUnivariate.R R/callPeaksMultivariate.R R/summarize.R R/global.R R/unis2pseudomulti.R R/combinatorialStates.R R/timedMessage.R R/scores.R R/stateswap.R R/binReads.R R/enrichmentAnalysis.R vignettes/PLOTS/H3K27me3-Adult-rep2_binsize150.pdf vignettes/PLOTS/H3K27me3-Adult-rep2_binsize1000.pdf man/model.combined.Rd man/simulateMultivariate.Rd man/plotHistograms.Rd man/plotting.Rd man/getStateColors.Rd man/getCombinations.Rd man/model.multivariate.Rd man/transitionFrequencies.Rd man/model.univariate.Rd man/scores.Rd man/experiment.table.Rd man/variableWidthBins.Rd man/simulateReadsFromCounts.Rd man/fixedWidthBins.Rd man/changePostCutoff.Rd man/callPeaksReplicates.Rd man/binned.data.Rd man/plotGenomeBrowser.Rd man/multivariateSegmentation.Rd man/callPeaksUnivariate.Rd man/simulateUnivariate.Rd man/heatmapCountCorrelation.Rd man/getDistinctColors.Rd man/subsample.Rd man/readBamFileAsGRanges.Rd man/readBedFileAsGRanges.Rd man/removeCondition.Rd man/callPeaksUnivariateAllChr.Rd man/Chromstar.Rd man/writeConfig.Rd man/print.uniHMM.Rd man/plotExpression.Rd man/print.combinedMultiHMM.Rd man/exportFiles.Rd man/changeMaxPostCutoff.Rd man/exportGRangesAsBedFile.Rd man/genes_rn4.Rd man/readCustomBedFile.Rd man/conversion.Rd man/mergeChroms.Rd man/loadHmmsFromFiles.Rd man/print.multiHMM.Rd man/genomicFrequencies.Rd man/chromstaR-objects.Rd man/callPeaksMultivariate.Rd man/readConfig.Rd man/zinbinom.Rd man/state.brewer.Rd man/multiHMM.Rd man/enrichment_analysis.Rd man/collapseBins.Rd man/uniHMM.Rd man/binReads.Rd man/combinatorialStates.Rd man/heatmapTransitionProbs.Rd man/combineMultivariates.Rd man/plotHistogram.Rd man/unis2pseudomulti.Rd man/combinedMultiHMM.Rd man/stateBrewer.Rd man/heatmapCombinations.Rd man/enrichmentAtAnnotation.Rd man/scanBinsizes.Rd man/chromstaR-package.Rd tests/testthat.R tests/testthat/test_stateBrewer.R tests/testthat/test_stateswap.R tests/testthat/test_scores.R inst/doc/chromstaR.pdf inst/doc/chromstaR.R