DESeqResMeta-class      An S4 class extending the DESeqResults object
                        containing additional fields for differential
                        expression data.
create_dir_struct       Initialize the directory structure for
                        automatically storing and structuring results.
create_master_res       Create a data set consisting of aggregated data
                        for multiple contrasts.
create_relabel_field    Create a new metadata field by renaming
                        existing levels of an existing field.
de_boxplot              Visualize differentially expressed genes as a
                        function of experimental design.
de_counts               Visualize differentially expressed gene counts
                        as a stacked barplot.
de_density_plot         Visualize density plots of fold-change or
                        significance values for aggregated data sets.
de_diverge_plot         Visualize fold-change divergence for
                        differentially expressed genes.
de_filter               Apply a custom fold-change filter to an
                        aggregated data frame.
de_heat                 Create heat maps of differentially expressed
                        genes.
de_profile_plot         Visualize gene-wise expression of
                        differentially expressed genes.
de_series               Identify and visualize patterns of expression
                        between differentially expressed genes across a
                        series of result sets.
de_volcano              Visualize the expression & significance of
                        differentially expressed genes.
enrich_res              Incorporate additional data about
                        differentially expressed genes into a DESeq2
                        result set.
exclude_data_subset     Select a subset of count and target data based
                        on metadata annotation.
get_de_data             Aggregate and retrieve data from multiple
                        differentially expressed result sets.
init_cutoffs            Initialize cutoff values for significance and
                        fold-change filtering.
init_data_paths         Initialize data paths for count and target
                        files.
keep_data_subset        Select a subset of count and target data based
                        on metadata annotation.
make_composite_field    Create a composite metadata field by merging
                        existing data.
plot_dendro             Create dendrograms based on hierarchical
                        clustering.
plot_euclid_dist        Visualize the Euclidian distances between
                        samples.
plot_gene               Visualize the expression of a specific gene
                        with regard to metadata grouping.
plot_group_stats        Visualize overall data set as a function of a
                        metadata grouping.
plot_mds                Visualize multi-dimensional scaled data for all
                        samples, with group-wise metadata incorporated
                        as colors and shapes.
plot_mds_hulls          Visualize multi-dimensional scaled data for all
                        samples, with group-wise metadata incorporated
                        as colors, shapes, and convex hulls.
plot_poisson_dist       Visualize the poisson distances between
                        samples.
prep_counts             Read tab or comma delimited count data.
prep_dds_from_data      Prepare a DESeq2 object based on count and
                        target data.
prep_targets            Read tab or comma delimited target metadata
                        file.
set_output_mode         Determine if visualizations are written to
                        file, printed to screen, or both.
transpose_gene_ids      Rename gene IDs based on a 1-to-1 mapping file.
write_all_de_results    Write differentially expressed gene data for
                        multiple result sets to file.
