ECDF                    Create ECDF plot of a sample against a
                        reference
MAplot                  Create a MA plot
MAvalues                Create values (M and A) for MA plot
barplot_samples_memi    Barplot of number of measured/missing features
                        of samples
batchCorrectionAssay    Remove batch effects from (count/intensity)
                        values of a 'SummarizedExperiment'
biocrates               Convert Biocrates xlsx output to
                        'SummarizedExperiment' object
createDfFeature         Create data frame of (count/intensity) values
                        for a selected feature along data processing
                        steps
create_boxplot          Create a boxplot of (count/intensity) values
                        per sample
cv                      Calculate coefficient of variation
cvFeaturePlot           Plot of feature-wise coefficient of variation
                        values
distSample              Create a heatmap using distance information
                        between samples
distShiny               Create distance matrix from numerical matrix
driftPlot               Plot the trend line for aggregated values
explVar                 Retrieve the explained variance for each
                        principal component (PCA) or axis (PCoA)
extractComb             Obtain the features that are present in a
                        specified set
featurePlot             Create a plot of (count/intensity) values over
                        the samples
hist_feature            Histogram for measured value per feature
hist_feature_category   Histogram of features per sample type
hist_sample             Plot a histogram of the number of a category
hist_sample_num         Return the number of a category
hoeffDPlot              Create a plot from a list of Hoeffding's D
                        values
hoeffDValues            Create values of Hoeffding's D statistics from
                        M and A values
imputeAssay             Impute missing values in a 'matrix'
maxQuant                Convert MaxQuant xlsx output to
                        'SummarizedExperiment' object
measured_category       Obtain the number of measured intensities per
                        sample type
mosaic                  Mosaic plot for two factors in colData(se)
normalizeAssay          Normalize a data sets (reduce technical sample
                        effects)
ordination              Dimensionality reduction with ordination
                        methods PCA, PCoA, NMDS, UMAP and tSNE
ordinationPlot          Plot the coordinates from 'ordination' values
permuteExplVar          Permute the expression values and retrieve the
                        explained variance
plotCV                  Plot CV values
plotPCALoadings         Plot for PCA loadings of features
plotPCAVar              Plot of explained variance against the
                        principal components
plotPCAVarPvalue        Plot p-values for the significance of principal
                        components
samples_memi            Create tibble containing number of
                        measured/missing features of samples
shinyQC                 Shiny application for initial QC exploration of
                        -omics data sets
sumDistSample           Plot the sum of distances to other samples
tblPCALoadings          Return tibble with PCA loadings for features
transformAssay          Transform the (count/intensity) values of a
                        'data.frame', 'tbl' or 'matrix'
upset_category          UpSet plot to display measures values across
                        sample types
volcanoPlot             Volcano plot of fold changes/differences
                        against p-values
