├── .Rbuildignore ├── .github └── workflows │ └── test.yml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── Makefile ├── NAMESPACE ├── R ├── 01_hpgltools.R ├── alt_splicing.R ├── annotation_biomart.R ├── annotation_genbank.R ├── annotation_gff.R ├── annotation_kegg.R ├── annotation_microbesonline.R ├── annotation_orgdb.R ├── annotation_shared.R ├── annotation_txt.R ├── annotation_uniprot.R ├── classify.R ├── de_basic.R ├── de_deseq.R ├── de_ebseq.R ├── de_edger.R ├── de_limma.R ├── de_noiseq.R ├── de_plots.R ├── de_shared.R ├── de_varpart.R ├── de_xlsx.R ├── dimension_reduction.R ├── expt.R ├── gene_sets.R ├── gsva.R ├── helpers_misc.R ├── metadata.R ├── model_testing.R ├── model_varpartition.R ├── motif.R ├── network.R ├── normalize_batch.R ├── normalize_convert.R ├── normalize_filter.R ├── normalize_norm.R ├── normalize_shared.R ├── normalize_transform.R ├── ontology_clusterprofiler.R ├── ontology_goseq.R ├── ontology_gostats.R ├── ontology_gprofiler.R ├── ontology_kegg.R ├── ontology_plots.R ├── ontology_shared.R ├── ontology_topgo.R ├── ontology_xlsx.R ├── pcr.R ├── peptides.R ├── phylo.R ├── plot_bar.R ├── plot_circos.R ├── plot_distribution.R ├── plot_dotplot.R ├── plot_genplot.R ├── plot_heatmap.R ├── plot_hist.R ├── plot_misc.R ├── plot_point.R ├── plot_proteomics.R ├── plot_shared.R ├── plot_venn.R ├── power_estimation.R ├── proteomics.R ├── se.R ├── sequence.R ├── shiny.R ├── singlecell.R ├── tf.R ├── tnseq.R ├── variants.R ├── xlsx.R ├── zzz_methods.R ├── zzz_print.R └── zzz_subset.R ├── README.md ├── TODO.md ├── hpgltools.Rproj ├── inst ├── bin │ └── shiny_start.R ├── doc │ ├── a-01_bacterial_example.R │ ├── a-01_bacterial_example.Rmd │ ├── a-01_bacterial_example.html │ ├── b-02_fission_data_exploration.R │ ├── b-02_fission_data_exploration.Rmd │ ├── b-02_fission_data_exploration.html │ ├── c-03_fission_differential_expression.R │ ├── c-03_fission_differential_expression.Rmd │ ├── c-03_fission_differential_expression.html │ ├── d-04_pasilla.R │ ├── d-04_pasilla.Rmd │ ├── d-04_pasilla.html │ └── reference.pdf └── shiny │ ├── expt_app_helpers.R │ ├── server.R │ └── ui.R ├── man ├── add_binary_states.Rd ├── add_clonotype_annotations.Rd ├── add_conditional_nas.Rd ├── all_adjusters.Rd ├── all_gprofiler.Rd ├── all_ontology_searches.Rd ├── all_pairwise.Rd ├── annotate_network.Rd ├── annotate_network_df.Rd ├── annotation-expt-method.Rd ├── annotation-set-expt-ANY-method.Rd ├── assay-ExpressionSet-ANY-method.Rd ├── assay-expt-ANY-method.Rd ├── assay-set-ExpressionSet-ANY-method.Rd ├── assay-set-expt-ANY-method.Rd ├── backup_expression_data-ExpressionSet-method.Rd ├── backup_expression_data-SummarizedExperiment-method.Rd ├── backup_expression_data.Rd ├── backup_file.Rd ├── base_size.Rd ├── basic_pairwise.Rd ├── batch_counts.Rd ├── binary_pairwise.Rd ├── bioc_all.Rd ├── calculate_aucc.Rd ├── cbcb_batch.Rd ├── cbcb_combat.Rd ├── cbcb_filter_counts.Rd ├── cheap_tm.Rd ├── check_circos.Rd ├── check_includes.Rd ├── check_metadata_year.Rd ├── check_plot_scale.Rd ├── check_xlsx_worksheet.Rd ├── choose_basic_dataset.Rd ├── choose_binom_dataset.Rd ├── choose_dataset.Rd ├── choose_limma_dataset.Rd ├── choose_model.Rd ├── choose_sequence_regions.Rd ├── circos-class.Rd ├── circos_arc.Rd ├── circos_check_chromosomes.Rd ├── circos_heatmap.Rd ├── circos_hist.Rd ├── circos_ideogram.Rd ├── circos_karyotype.Rd ├── circos_make.Rd ├── circos_plus_minus.Rd ├── circos_prefix.Rd ├── circos_suffix.Rd ├── circos_ticks.Rd ├── circos_tile.Rd ├── classify_n_times.Rd ├── classify_variants.Rd ├── clear_session.Rd ├── cleavage_histogram.Rd ├── cluster_trees.Rd ├── colData-ExpressionSet-method.Rd ├── colData-expt-method.Rd ├── colData-set-ExpressionSet-ANY-method.Rd ├── colData-set-expt-ANY-method.Rd ├── color_int.Rd ├── colors-SummarizedExperiment-method.Rd ├── colors-expt-method.Rd ├── colors-set-SummarizedExperiment-method.Rd ├── colors-set-expt-method.Rd ├── colors-set.Rd ├── colors.Rd ├── column_assignment.Rd ├── combine_de_tables.Rd ├── combine_expts.Rd ├── combine_extracted_plots.Rd ├── combine_mapped_table.Rd ├── combine_single_de_table.Rd ├── compare_batches.Rd ├── compare_de_results.Rd ├── compare_de_tables.Rd ├── compare_go_searches.Rd ├── compare_logfc_plots.Rd ├── compare_pc_sv.Rd ├── compare_significant_contrasts.Rd ├── compare_surrogate_estimates.Rd ├── concatenate_runs.Rd ├── convert_counts.Rd ├── convert_gsc_ids.Rd ├── convert_ids.Rd ├── cordist.Rd ├── correlate_de_tables.Rd ├── count_clonotype_by_cluster.Rd ├── count_expt_snps.Rd ├── count_nmer-character-method.Rd ├── count_nmer.Rd ├── counts_from_surrogates.Rd ├── cp_options.Rd ├── create_expt.Rd ├── create_partitions.Rd ├── create_scd.Rd ├── create_se.Rd ├── de_venn.Rd ├── default_proper.Rd ├── deparse_go_value.Rd ├── deseq2_pairwise.Rd ├── deseq_lrt.Rd ├── deseq_pairwise.Rd ├── deseq_try_sv.Rd ├── disjunct_pvalues.Rd ├── dispatch_count_lines.Rd ├── dispatch_csv_search.Rd ├── dispatch_fasta_lengths.Rd ├── dispatch_filename_search.Rd ├── dispatch_gc.Rd ├── dispatch_metadata_extract.Rd ├── dispatch_metadata_ratio.Rd ├── dispatch_regex_search.Rd ├── divide_seq.Rd ├── do_batch.Rd ├── do_pairwise.Rd ├── do_topgo.Rd ├── dopar.Rd ├── dot-data.Rd ├── download_gbk.Rd ├── download_microbesonline_files.Rd ├── dream_pairwise.Rd ├── ebseq_few.Rd ├── ebseq_pairwise.Rd ├── ebseq_pairwise_subset.Rd ├── ebseq_size_factors.Rd ├── ebseq_two.Rd ├── edger_pairwise.Rd ├── enrichResult.Rd ├── exclude_genes_expt.Rd ├── exprs-SummarizedExperiment-method.Rd ├── exprs-expt-method.Rd ├── exprs-set-ExpressionSet-data.frame-method.Rd ├── exprs-set-SummarizedExperiment-ANY-method.Rd ├── exprs-set-expt-ANY-method.Rd ├── expt.Rd ├── extract_abundant_genes.Rd ├── extract_coefficient_scatter.Rd ├── extract_de_plots.Rd ├── extract_go.Rd ├── extract_interesting_goseq.Rd ├── extract_keepers.Rd ├── extract_lengths.Rd ├── extract_mayu_pps_fdr.Rd ├── extract_metadata.Rd ├── extract_msraw_data.Rd ├── extract_mzML_scans.Rd ├── extract_mzXML_scans.Rd ├── extract_peprophet_data.Rd ├── extract_pyprophet_data.Rd ├── extract_scan_data.Rd ├── extract_siggenes.Rd ├── extract_significant_genes.Rd ├── fData-SummarizedExperiment-method.Rd ├── fData-expt-method.Rd ├── fData-set-SummarizedExperiment-ANY-method.Rd ├── fData-set-expt-ANY-method.Rd ├── factor_rsquared.Rd ├── features_greater_than.Rd ├── features_in_single_condition.Rd ├── features_less_than.Rd ├── filter_counts.Rd ├── filter_scd.Rd ├── find_subseq_target_temp.Rd ├── find_working_dataset.Rd ├── find_working_mart.Rd ├── flanking_sequence.Rd ├── gather_cp_genes.Rd ├── gather_eupath_utrs_padding.Rd ├── gather_genes_orgdb.Rd ├── gather_masses.Rd ├── gather_ontology_genes.Rd ├── gather_preprocessing_metadata.Rd ├── gather_utrs_padding.Rd ├── gather_utrs_txdb.Rd ├── genefilter_cv_counts.Rd ├── genefilter_kofa_counts.Rd ├── genefilter_pofa_counts.Rd ├── generate_expt_colors.Rd ├── generate_nn_groups.Rd ├── genomic_kmer_dist.Rd ├── genoplot_chromosome.Rd ├── getEdgeWeights.Rd ├── get_abundant_genes.Rd ├── get_backup_expression_data-ExpressionSet-method.Rd ├── get_backup_expression_data-SummarizedExperiment-method.Rd ├── get_backup_expression_data.Rd ├── get_expt_colors.Rd ├── get_genesizes.Rd ├── get_git_commit.Rd ├── get_group_gsva_means.Rd ├── get_gsvadb_names.Rd ├── get_identifier.Rd ├── get_individual_snps.Rd ├── get_kegg_compounds.Rd ├── get_kegg_genes.Rd ├── get_kegg_orgn.Rd ├── get_kegg_sub.Rd ├── get_microbesonline_taxid.Rd ├── get_msigdb_metadata.Rd ├── get_pairwise_gene_abundances.Rd ├── get_plot_columns.Rd ├── get_proportion_snp_sets.Rd ├── get_res.Rd ├── get_sig_genes.Rd ├── get_sig_gsva_categories.Rd ├── get_snp_sets.Rd ├── get_yyyymm_commit.Rd ├── gff2gr.Rd ├── gff2irange.Rd ├── ggplotly_url.Rd ├── ggplt.Rd ├── godef.Rd ├── golev.Rd ├── golevel.Rd ├── golevel_df.Rd ├── goont.Rd ├── gosec.Rd ├── goseq2enrich.Rd ├── goseq_msigdb.Rd ├── goseq_table.Rd ├── goseq_trees.Rd ├── gostats2enrich.Rd ├── gostats_kegg.Rd ├── gostats_trees.Rd ├── gosyn.Rd ├── goterm.Rd ├── gotest.Rd ├── gprofiler2enrich.Rd ├── grapes-colon-colon-colon-grapes.Rd ├── graph_metrics.Rd ├── group_mean_cds_length.Rd ├── guess_orgdb_keytype.Rd ├── heatmap.3.Rd ├── hpgl_GOplot.Rd ├── hpgl_GroupDensity.Rd ├── hpgl_arescore.Rd ├── hpgl_cor.Rd ├── hpgl_dist.Rd ├── hpgl_filter_counts.Rd ├── hpgl_log2cpm.Rd ├── hpgl_norm.Rd ├── hpgl_padjust.Rd ├── hpgl_qshrink.Rd ├── hpgl_qstats.Rd ├── hpgl_rpkm.Rd ├── hpgl_voom.Rd ├── hpgl_voomweighted.Rd ├── hpgltools.Rd ├── iDA-matrix-method.Rd ├── iDA.Rd ├── ihw_adjust.Rd ├── import_deseq.Rd ├── import_edger.Rd ├── impute_expt.Rd ├── init_xlsx.Rd ├── intersect_signatures.Rd ├── intersect_significant.Rd ├── kegg_vector_to_df.Rd ├── limma_pairwise.Rd ├── load_annotations.Rd ├── load_biomart_annotations.Rd ├── load_biomart_go.Rd ├── load_biomart_orthologs.Rd ├── load_genbank_annotations.Rd ├── load_gff_annotations.Rd ├── load_gmt_signatures.Rd ├── load_kegg_annotations.Rd ├── load_microbesonline_annotations.Rd ├── load_microbesonline_go.Rd ├── load_orgdb_annotations.Rd ├── load_orgdb_go.Rd ├── load_trinotate_annotations.Rd ├── load_trinotate_go.Rd ├── load_uniprot_annotations.Rd ├── load_uniprot_go.Rd ├── loadme.Rd ├── local_get_value.Rd ├── make_assembly_spec.Rd ├── make_dnaseq_spec.Rd ├── make_gsc_from_abundant.Rd ├── make_gsc_from_ids.Rd ├── make_gsc_from_pairwise.Rd ├── make_id2gomap.Rd ├── make_kegg_df.Rd ├── make_limma_tables.Rd ├── make_pairwise_contrasts.Rd ├── make_pombe_expt.Rd ├── make_pombe_se.Rd ├── make_rnaseq_spec.Rd ├── make_simplified_contrast_matrix.Rd ├── make_tx_gene_map.Rd ├── map_keepers.Rd ├── map_kegg_dbs.Rd ├── map_orgdb_ids.Rd ├── mean_by_bioreplicate.Rd ├── mean_by_factor.Rd ├── median_by_factor.Rd ├── mesg.Rd ├── model_test.Rd ├── my_identifyAUBlocks.Rd ├── my_isva.Rd ├── my_runsims.Rd ├── mymakeContrasts.Rd ├── myretrieveKGML.Rd ├── network_from_matrix.Rd ├── noiseq_pairwise.Rd ├── normalize.Rd ├── normalize_counts.Rd ├── normalize_expt.Rd ├── normalize_se.Rd ├── notes-expt-method.Rd ├── orgdb_from_ah.Rd ├── overlap_geneids.Rd ├── overlap_groups.Rd ├── pData-SummarizedExperiment-method.Rd ├── pData-expt-method.Rd ├── pData-set-SummarizedExperiment-ANY-method.Rd ├── pData-set-expt-ANY-method.Rd ├── parse_msigdb.Rd ├── parse_msigdb_sqlite.Rd ├── parse_msigdb_xml.Rd ├── pattern_count_genome.Rd ├── pca_highscores.Rd ├── pca_information.Rd ├── pct_all_kegg.Rd ├── pct_kegg_diff.Rd ├── pipe.Rd ├── please_install.Rd ├── plot_3d_pca.Rd ├── plot_batchsv.Rd ├── plot_bcv.Rd ├── plot_boxplot.Rd ├── plot_cleaved.Rd ├── plot_corheat.Rd ├── plot_de_pvals.Rd ├── plot_density.Rd ├── plot_disheat.Rd ├── plot_dist_scatter.Rd ├── plot_enrichresult.Rd ├── plot_epitrochoid.Rd ├── plot_essentiality.Rd ├── plot_fun_venn.Rd ├── plot_goseq_pval.Rd ├── plot_gostats_pval.Rd ├── plot_gprofiler2_pval.Rd ├── plot_gprofiler_pval.Rd ├── plot_heatmap-ExpressionSet-method.Rd ├── plot_heatmap-SummarizedExperiment-method.Rd ├── plot_heatmap-data.frame-method.Rd ├── plot_heatmap-expt-method.Rd ├── plot_heatmap.Rd ├── plot_heatplus.Rd ├── plot_histogram.Rd ├── plot_hypotrochoid.Rd ├── plot_intensity_mz.Rd ├── plot_legend.Rd ├── plot_libsize-ExpressionSet-ANY-ANY-method.Rd ├── plot_libsize-SummarizedExperiment-ANY-ANY-method.Rd ├── plot_libsize-data.frame-factor-character-method.Rd ├── plot_libsize-expt-ANY-ANY-method.Rd ├── plot_libsize.Rd ├── plot_libsize_prepost.Rd ├── plot_linear_scatter.Rd ├── plot_ly.Rd ├── plot_ma_condition_de.Rd ├── plot_ma_de.Rd ├── plot_meta_sankey-expt-method.Rd ├── plot_meta_sankey.Rd ├── plot_metadata_factors.Rd ├── plot_multihistogram.Rd ├── plot_multiplot.Rd ├── plot_mzxml_boxplot.Rd ├── plot_nonzero-ExpressionSet-method.Rd ├── plot_nonzero-SummarizedExperiment-method.Rd ├── plot_nonzero-expt-method.Rd ├── plot_nonzero.Rd ├── plot_num_siggenes.Rd ├── plot_ontpval.Rd ├── plot_pairwise_ma.Rd ├── plot_pca.Rd ├── plot_pca_genes.Rd ├── plot_pcfactor.Rd ├── plot_pcload.Rd ├── plot_pcs.Rd ├── plot_pct_kept.Rd ├── plot_peprophet_data.Rd ├── plot_pyprophet_counts.Rd ├── plot_pyprophet_distribution.Rd ├── plot_pyprophet_points.Rd ├── plot_pyprophet_protein.Rd ├── plot_pyprophet_xy.Rd ├── plot_qq_all.Rd ├── plot_rmats.Rd ├── plot_rpm.Rd ├── plot_sample_bars.Rd ├── plot_sample_cvheatmap.Rd ├── plot_sample_heatmap-ExpressionSet-method.Rd ├── plot_sample_heatmap-SummarizedExperiment-method.Rd ├── plot_sample_heatmap-expt-method.Rd ├── plot_sample_heatmap.Rd ├── plot_sankey_de.Rd ├── plot_scatter.Rd ├── plot_seurat_scatter.Rd ├── plot_significant_bar.Rd ├── plot_single_qq.Rd ├── plot_sm-ExpressionSet-method.Rd ├── plot_sm-SummarizedExperiment-method.Rd ├── plot_sm-data.frame-method.Rd ├── plot_sm-expt-method.Rd ├── plot_sm.Rd ├── plot_spirograph.Rd ├── plot_suppa.Rd ├── plot_svfactor.Rd ├── plot_topgo_densities.Rd ├── plot_topgo_pval.Rd ├── plot_topn.Rd ├── plot_tsne.Rd ├── plot_variance_coefficients-ExpressionSet-method.Rd ├── plot_variance_coefficients-SummarizedExperiment-method.Rd ├── plot_variance_coefficients-expt-method.Rd ├── plot_variance_coefficients.Rd ├── plot_volcano_condition_de.Rd ├── plot_volcano_de.Rd ├── plotly_pca.Rd ├── pp.Rd ├── primer_qc.Rd ├── print.abundant_genes.Rd ├── print.all_gprofiler.Rd ├── print.all_pairwise.Rd ├── print.annotations_biomart.Rd ├── print.aucc_info.Rd ├── print.biomart_go.Rd ├── print.cds_variant_primers.Rd ├── print.classified_mutations.Rd ├── print.classifier_evaluation.Rd ├── print.clusterprofiler_result.Rd ├── print.combined_de.Rd ├── print.combined_table.Rd ├── print.correlation_heatmap.Rd ├── print.cross_table_comparison.Rd ├── print.density_plot.Rd ├── print.density_primers.Rd ├── print.deseq_lrt.Rd ├── print.distance_heatmap.Rd ├── print.expt.Rd ├── print.goseq_result.Rd ├── print.gostats_result.Rd ├── print.gprofiler_result.Rd ├── print.graphed_metrics.Rd ├── print.gsva_result.Rd ├── print.gsva_sig.Rd ├── print.legend_plot.Rd ├── print.libsize_plot.Rd ├── print.mapped_keepers.Rd ├── print.meta_sankey.Rd ├── print.nonzero_plot.Rd ├── print.partitioned_data.Rd ├── print.pattern_counted.Rd ├── print.pca_result.Rd ├── print.prepost_filter.Rd ├── print.preprocessing_metadata.Rd ├── print.proper_estimate.Rd ├── print.reordered_varpart.Rd ├── print.sig_genes.Rd ├── print.sig_intersect.Rd ├── print.snp_intersections.Rd ├── print.snp_sets.Rd ├── print.snps_genes.Rd ├── print.standardmedian_plot.Rd ├── print.topgo_result.Rd ├── print.topn_plot.Rd ├── print.varcoef_plot.Rd ├── print.varpart.Rd ├── print.written_expt.Rd ├── print.written_xlsx.Rd ├── print_ups_downs.Rd ├── proportions_by_factors.Rd ├── prune_network.Rd ├── pull_git_commit.Rd ├── random_ontology.Rd ├── rank_order_scatter.Rd ├── rbind_summary_rows.Rd ├── read_counts_expt.Rd ├── read_metadata.Rd ├── read_snp_columns.Rd ├── read_thermo_xlsx.Rd ├── recolor_points.Rd ├── record_seurat_samples.Rd ├── renderme.Rd ├── replot_varpart_percent.Rd ├── rex.Rd ├── rowData-ExpressionSet-method.Rd ├── rowData-expt-method.Rd ├── rowData-set-expt-method.Rd ├── rowMeans.Rd ├── rowmax_filter_counts.Rd ├── s2s_all_filters.Rd ├── sampleNames-SummarizedExperiment-method.Rd ├── sampleNames-expt-method.Rd ├── sampleNames-set-SummarizedExperiment-ANY-method.Rd ├── sampleNames-set-expt-ANY-method.Rd ├── sanitize_expt.Rd ├── sanitize_expt_fData.Rd ├── sanitize_expt_pData.Rd ├── sanitize_metadata.Rd ├── sanitize_number_encoding.Rd ├── sanitize_percent.Rd ├── saveme.Rd ├── score_gsva_likelihoods.Rd ├── score_mhess.Rd ├── self_evaluate_model.Rd ├── semantic_copynumber_extract.Rd ├── semantic_copynumber_filter.Rd ├── semantic_expt_filter.Rd ├── sequence_attributes.Rd ├── sequential_variants.Rd ├── set_expt_batches.Rd ├── set_expt_colors.Rd ├── set_expt_conditions.Rd ├── set_expt_factors.Rd ├── set_expt_genename_column.Rd ├── set_expt_genenames.Rd ├── set_expt_samplenames.Rd ├── shiny.Rd ├── sig_ontologies.Rd ├── significant_barplots.Rd ├── sillydist.Rd ├── simple_clusterprofiler.Rd ├── simple_cp_enricher.Rd ├── simple_dorothea.Rd ├── simple_filter_counts.Rd ├── simple_gadem.Rd ├── simple_goseq.Rd ├── simple_gostats.Rd ├── simple_gprofiler.Rd ├── simple_gprofiler2.Rd ├── simple_gprofiler_old.Rd ├── simple_gsva.Rd ├── simple_motifRG.Rd ├── simple_pathview.Rd ├── simple_proper.Rd ├── simple_topgo-character-method.Rd ├── simple_topgo.Rd ├── simple_varpart.Rd ├── simple_xcell.Rd ├── single_topgo_tree.Rd ├── skim_seurat_metadata.Rd ├── slide_de_threshold.Rd ├── sm.Rd ├── snp_by_chr.Rd ├── snp_cds_primers.Rd ├── snp_density_primers.Rd ├── snp_subset_genes.Rd ├── snpnames2gr.Rd ├── snps_intersections.Rd ├── snps_vs_genes.Rd ├── snps_vs_genes_padded.Rd ├── state-SummarizedExperiment-method.Rd ├── state-expt-method.Rd ├── state-set-SummarizedExperiment-method.Rd ├── state-set-expt-method.Rd ├── state-set.Rd ├── state.Rd ├── steal_salmon_tx_ids.Rd ├── sub-.expt.Rd ├── sub-sub-expt-character-ANY-method.Rd ├── subset_expt-SummarizedExperiment-method.Rd ├── subset_expt.Rd ├── subset_genes.Rd ├── subset_ontology_search.Rd ├── subtract_expt.Rd ├── sum_eupath_exon_counts.Rd ├── sum_exon_widths.Rd ├── summarize_scd_clusters.Rd ├── summarize_ups_downs.Rd ├── sva_modify_pvalues.Rd ├── synchronize_expt.Rd ├── table_style.Rd ├── tar_meta_column.Rd ├── tempfile.Rd ├── tmpmd5file.Rd ├── tnseq_multi_saturation.Rd ├── tnseq_saturation.Rd ├── topDiffGenes.Rd ├── topgo2enrich.Rd ├── topgo_tables.Rd ├── topgo_trees.Rd ├── transform_counts.Rd ├── u_plot.Rd ├── unAsIs.Rd ├── upsetr_combined_de.Rd ├── upsetr_sig.Rd ├── variance_expt.Rd ├── varpart_summaries.Rd ├── verbose.Rd ├── wgcna_network.Rd ├── what_happened.Rd ├── write_basic.Rd ├── write_cds_entries.Rd ├── write_classifier_summary.Rd ├── write_combined_legend.Rd ├── write_combined_summary.Rd ├── write_cp_data.Rd ├── write_de_table.Rd ├── write_density_primers.Rd ├── write_deseq.Rd ├── write_edger.Rd ├── write_expt.Rd ├── write_go_xls.Rd ├── write_goseq_data.Rd ├── write_gostats_data.Rd ├── write_gprofiler_data.Rd ├── write_gsva.Rd ├── write_limma.Rd ├── write_sample_design.Rd ├── write_sig_legend.Rd ├── write_snps.Rd ├── write_subset_ontologies.Rd ├── write_suppa_table.Rd ├── write_topgo_data.Rd ├── write_xlsx-ANY-ANY-ANY-written_xlsx-method.Rd ├── write_xlsx.Rd ├── xlsx_insert_png.Rd ├── xref_regions.Rd └── ymxb_print.Rd ├── tests ├── testthat.R └── testthat │ ├── test_001load_package.R │ ├── test_002load_data.R │ ├── test_005_annotation_biomart.R │ ├── test_015annotation_genbank.R │ ├── test_020annotation_gff.R │ ├── test_025annotation_kegg.R │ ├── test_030annotation_microbesonline.R │ ├── test_040annotation_orgdb.R │ ├── test_045annotation_shared.R │ ├── test_050annotation_txt.R │ ├── test_055annotation_uniprot.R │ ├── test_060expt.R │ ├── test_061se.R │ ├── test_065de_all.R │ ├── test_066power_estimation.R │ ├── test_105helpers_misc.R │ ├── test_115dimension_reduction.R │ ├── test_125model_testing.R │ ├── test_135model_varpartition.R │ ├── test_145nmer.R │ ├── test_150normalize_batch.R │ ├── test_155normalize_convert.R │ ├── test_160normalize_filter.R │ ├── test_165normalize_norm.R │ ├── test_175normalize_transform.R │ ├── test_180ontology_all.R │ ├── test_185sequence_queries.R │ ├── test_225plot_bar.R │ ├── test_240plot_dotplot.R │ ├── test_245gsva.R │ ├── test_250proteomics.R │ ├── test_260variants.R │ ├── test_270motif.R │ ├── test_280tnseq.R │ ├── test_290splicing.R │ ├── test_302graph_metrics.R │ ├── test_310norm_shared.R │ ├── test_311norm_convert.R │ ├── test_312norm_normalize.R │ ├── test_313norm_transform.R │ ├── test_314norm_filter.R │ ├── test_315norm_batch.R │ ├── test_318norm_surrogates.R │ ├── test_320de_limma_batch.R │ ├── test_321de_limma_combat.R │ ├── test_322de_intnoint_limma.R │ ├── test_324de_deseq.R │ ├── test_326de_edger.R │ ├── test_327de_basic.R │ ├── test_329de_shared.R │ ├── test_400paeruginosa.R │ ├── test_415solanum_betaceum.R │ ├── test_419varpart.R │ └── test_470expt_spyogenes.R └── vignettes ├── a-01_bacterial_example.Rmd ├── 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