bushmanplot             Create a stacked area plot that represents the
                        abundance of integration sites over time.
bw                      Calculate the bw index
convert_columnwise_relative
                        Converts a matrix to relative abundances
evaluate_clustering     Evaluate a clustering using the given method
evaluate_clustering_bw
                        Evaluate a clustering using the bw index
evaluate_clustering_custom
                        Evaluate a clustering using a custom evaluation
                        function
evaluate_clustering_dunn
                        Evaluate a clustering using the dunn index
evaluate_clustering_ptbiserial
                        Evaluate a clustering using the point-biserial
                        index
evaluate_clustering_sdindex
                        Evaluate a clustering using the SD-index
evaluate_clustering_silhouette
                        Evaluate a clustering using the silhouette
                        index
filter_at_tp_biggest_n
                        Filters a matrix of readouts for the n biggest
                        IS at a certain measurement
filter_at_tp_min        Filters a matrix of readouts for IS that have a
                        minimum occurrence in some measurement
filter_combine_measurements
                        Combines columns that have the same name. The
                        columns are joined additively.
filter_is_names         Shortens the rownames of a readout matrix to
                        the shortest distinct prefix
filter_match            Filters for columns containing a certain
                        substring.
filter_measurement_names
                        Splits a vector of strings by a given regexp,
                        selects and rearranges the parts and joins them
                        again
filter_names            Filters a vector of names and returns the
                        shortest common prefix.
filter_nr_tp_min        Filters for a minimum number of time
                        points/measurements
filter_zero_columns     Removes columns that only contain 0 or NA.
filter_zero_rows        Removes rows that only contain 0 or NA.
find_best_nr_cluster    Finds the best number of clusters according to
                        silhouette
get_similarity_matrix   Generate a similarity matrix
ggplot_colors           Get the default ggplot color palette or a color
                        palette based on the ggplot palette, but with
                        sub-colors that differ in their luminance
lineplot_split_clone    Show line plots of all integration sites over
                        time, split into facets by their respective
                        clone.
normalize_timecourse    Normalizes a time course using a given mapping
                        from integration sites to clones.
plot.ISSimilarity       Plots the similarity of integration sites
plot.clusterObj         Plots the clustering based on a clustering
                        object
plot.timeseries         Plots time series data, which consists of
                        multiple measurements over time / place (cols)
                        of different clones / integration sites (rows).
plot_rsquare            Plots R^2 of two integration sites
reconstruct             Apply a clustering algorithm to a given time
                        course.
reconstruct_kmedoid     Calculate the k-medoids clustering for a given
                        time course.
reconstruct_recursive   Apply a clustering algorithm recursively to a
                        given time course.
weighted_spring_model   Plot the relationship of integration sites as a
                        graph.
