Function reference
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applyNormalization() - Applies normalization methods to given data set
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assessNormalization() - Data-driven miRNA sequencing Normalization Assessment
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defineClusters() - Polycistronic clustering of miRNAs
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defineControls() - Definition of negative and positive control miRNAs for DANA normalization assessment
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listClusters() - Convert gene-wise clusters into nested list
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miRNA.coordinates - Chromosomal coordinate for miRNA (hsa) from MiRBase v22
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norm.DESeq() - DESeq Normalization
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norm.Med() - Median (Med) Normalization
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norm.PoissonSeq() - PoissonSeq Normalization
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norm.QN() - Quantile Normalization (QN)
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norm.RUV() - Normalization By Remove Unwanted Variation (RUV)
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norm.TC() - Total Count (TC) Normalization
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norm.TMM() - Trimmed Mean of M-values (TMM) Normalization
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norm.UQ() - Upper Quartile (UQ) Normalization
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partialCor() - Partial correlation estimation
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pearsonCor() - Pearson correlation estimation
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plotCor() - Correlation plot for partial correlations within polycistronic clusters
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plotCountHist() - Read count histogram
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plotDANA() - Scatter plot DANA assessment metrics
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plotMeanSD() - Mean-Standard Deviation Plot
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prec2corr() - Computes partial correlation matrix from a given precision matrix