| create_dir_struct | Initialize the directory structure for automatically storing... |
| create_master_res | Create a data set consisting of aggregated data for multiple... |
| create_relabel_field | Create a new metadata field by renaming existing levels of an... |
| de_boxplot | Visualize differentially expressed genes as a function of... |
| de_counts | Visualize differentially expressed gene counts as a stacked... |
| de_density_plot | Visualize density plots of fold-change or significance values... |
| de_diverge_plot | Visualize fold-change divergence for differentially expressed... |
| de_filter | Apply a custom fold-change filter to an aggregated data... |
| de_heat | Create heat maps of differentially expressed genes. |
| de_profile_plot | Visualize gene-wise expression of differentially expressed... |
| DESeqResMeta-class | An S4 class extending the DESeqResults object containing... |
| de_series | Identify and visualize patterns of expression between... |
| de_volcano | Visualize the expression & significance of differentially... |
| enrich_res | Incorporate additional data about differentially expressed... |
| exclude_data_subset | Select a subset of count and target data based on metadata... |
| get_de_data | Aggregate and retrieve data from multiple differentially... |
| init_cutoffs | Initialize cutoff values for significance and fold-change... |
| 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... |
| 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... |
| plot_group_stats | Visualize overall data set as a function of a metadata... |
| plot_mds | Visualize multi-dimensional scaled data for all samples, with... |
| plot_mds_hulls | Visualize multi-dimensional scaled data for all samples, with... |
| 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... |
| 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... |
