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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(amariDistance)
export(attributeComparisonSignatures)
export(build_granges_object)
export(calculate_FI)
export(calculate_for_classifier_range)
export(computeAbsDelta4OptK)
export(computeAmariDistances)
export(computeCopheneticCoeff)
export(computeEntropy4OptK)
export(computeFeatureStats)
export(computeFisher4Regions)
export(computeFrobErrorStats)
export(computeMeanDiff4SignatureCombs)
export(computeNES)
export(computePValue4FrobError)
export(computePeakStats4Regions)
export(computeRecoveryAUC)
export(computeRegionFC)
export(computeRegionFC4GRlist)
export(computeRmdAUCs)
export(computeRunningPeakStats4Regions)
export(computeSignatureSpecificFeatures)
export(computeSilhoutteWidth)
export(cosineDiss)
export(cosineDissMat)
export(cosineDist)
export(cosineSim)
export(extract_signature_specific_genes)
export(filter_features)
export(filter_specific_features)
export(generateRiverplot)
export(generate_classifier)
export(getColorAnno)
export(getColorMap)
export(getIndex4SignatureCombs)
export(getSignatureCombCounts)
export(getSignatureNames)
export(igvCoord2Grange)
export(match_and_count)
export(merge.nmf)
export(nmfExperimentFromFile)
export(nmfExperimentFromMatrix)
export(normalizeH)
export(normalizeUpperQuartile)
export(normalizeW)
export(orderBinary)
export(performRowKmeans)
export(plotHMatrix)
export(plotHeatmap4MatrixList)
export(plotKStats)
export(plotRankedFrobErrors)
export(plotSignatureFeatures)
export(proposeOptK)
export(rankTransform)
export(regularizeH)
export(relabelRiverplot)
export(runNmfGpu)
export(runNmfGpuPyCuda)
export(science_theme)
export(sigmoidTransform)
export(sigmoidTransform2)
export(translateBratwurstToYAPSA)
exportClasses(nmfExperiment)
exportMethods(FeatureStats)
exportMethods(FrobError)
exportMethods(HMatrix)
exportMethods(HMatrixList)
exportMethods(OptK)
exportMethods(OptKStats)
exportMethods(SignatureSpecificFeatures)
exportMethods(WMatrix)
exportMethods(WMatrixList)
exportMethods(setFeatureStats)
exportMethods(setFrobError)
exportMethods(setHMatrixList)
exportMethods(setOptK)
exportMethods(setOptKStats)
exportMethods(setSignatureSpecificFeatures)
exportMethods(setWMatrixList)
import(ComplexHeatmap)
import(GenomicRanges)
import(NMF)
import(RColorBrewer)
import(S4Vectors)
import(SummarizedExperiment)
import(cowplot)
import(ggplot2)
import(nnls)
import(reshape2)
import(riverplot)
importFrom(RcppCNPy,npyLoad)
importFrom(RcppCNPy,npySave)
importFrom(S4Vectors,DataFrame)
importFrom(YAPSA,normalize_df_per_dim)
importFrom(caret,confusionMatrix)
importFrom(circlize,colorRamp2)
importFrom(cluster,pam)
importFrom(cluster,silhouette)
importFrom(data.table,fread)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
importFrom(rtracklayer,import.bed)