Files in elsayed-lab/hpgltools

A pile of (hopefully) useful R functions

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