![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| 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 |
| ECDF | Create ECDF plot of a sample against a reference |
| 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' |
| MAplot | Create a MA plot |
| MAvalues | Create values (M and A) for MA plot |
| 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 |