| %:::% |
Man page
|
| %>% |
Man page
|
| %dopar% |
Man page
|
| .data |
Man page
|
| := |
Man page
|
| [.expt |
Man page
|
| [[,expt,character,ANY-method |
Man page
|
| `%:::%` |
Source code
|
| `[.expt` |
Source code
|
| `colors<-` |
Source code
|
| `state<-` |
Source code
|
| add_binary_states |
Man page
Source code
|
| add_clonotype_annotations |
Man page
Source code
|
| add_conditional_nas |
Man page
Source code
|
| all_adjusters |
Man page
Source code
|
| all_gprofiler |
Man page
Source code
|
| all_ontology_searches |
Man page
Source code
|
| all_pairwise |
Man page
Source code
|
| annotate_network |
Man page
Source code
|
| annotate_network_df |
Man page
Source code
|
| annotate_network_nodes |
Source code
|
| annotation,expt-method |
Man page
|
| annotation<-,expt,ANY-method |
Man page
|
| assay,ExpressionSet,ANY-method |
Man page
|
| assay,expt,ANY-method |
Man page
|
| assay<-,ExpressionSet,ANY-method |
Man page
|
| assay<-,expt,ANY-method |
Man page
|
| backup_expression_data |
Man page
Source code
|
| backup_expression_data,ExpressionSet-method |
Man page
|
| backup_expression_data,SummarizedExperiment-method |
Man page
|
| backup_file |
Man page
Source code
|
| base_size |
Man page
|
| basic_pairwise |
Man page
Source code
|
| batch_counts |
Man page
Source code
|
| binary_pairwise |
Man page
Source code
|
| bioc_all |
Man page
Source code
|
| calculate_aucc |
Man page
Source code
|
| cbcb_batch |
Man page
Source code
|
| cbcb_combat |
Man page
Source code
|
| cbcb_filter_counts |
Man page
Source code
|
| cheap_tm |
Man page
Source code
|
| check_circos |
Man page
Source code
|
| check_includes |
Man page
Source code
|
| check_metadata_year |
Man page
Source code
|
| check_plot_scale |
Man page
Source code
|
| check_single_de_table |
Source code
|
| check_xlsx_worksheet |
Man page
Source code
|
| choose_basic_dataset |
Man page
Source code
|
| choose_binom_dataset |
Man page
Source code
|
| choose_dataset |
Man page
Source code
|
| choose_limma_dataset |
Man page
Source code
|
| choose_model |
Man page
Source code
|
| choose_sequence_regions |
Man page
Source code
|
| circos-class |
Man page
|
| circos_arc |
Man page
Source code
|
| circos_check_chromosomes |
Man page
Source code
|
| circos_heatmap |
Man page
Source code
|
| circos_hist |
Man page
Source code
|
| circos_ideogram |
Man page
Source code
|
| circos_karyotype |
Man page
Source code
|
| circos_make |
Man page
Source code
|
| circos_plus_minus |
Man page
Source code
|
| circos_prefix |
Man page
Source code
|
| circos_suffix |
Man page
Source code
|
| circos_ticks |
Man page
Source code
|
| circos_tile |
Man page
Source code
|
| classify_n_times |
Man page
Source code
|
| classify_variants |
Man page
Source code
|
| clear_session |
Man page
Source code
|
| cleavage_histogram |
Man page
Source code
|
| cluster_trees |
Man page
Source code
|
| colData,ExpressionSet-method |
Man page
|
| colData,expt-method |
Man page
|
| colData<-,ExpressionSet,ANY-method |
Man page
|
| colData<-,expt,ANY-method |
Man page
|
| collect_gsc_ids_from_df |
Source code
|
| color_int |
Man page
Source code
|
| colors |
Man page
Source code
|
| colors,SummarizedExperiment-method |
Man page
|
| colors,expt-method |
Man page
|
| colors<- |
Man page
|
| colors<-,SummarizedExperiment-method |
Man page
|
| colors<-,expt-method |
Man page
|
| combine_de_tables |
Man page
Source code
|
| combine_expts |
Man page
Source code
|
| combine_extracted_plots |
Man page
Source code
|
| combine_mapped_table |
Man page
Source code
|
| combine_single_de_table |
Man page
Source code
|
| compare_batches |
Man page
Source code
|
| compare_de_results |
Man page
Source code
|
| compare_de_tables |
Man page
Source code
|
| compare_go_searches |
Man page
Source code
|
| compare_logfc_plots |
Man page
Source code
|
| compare_pc_sv |
Man page
Source code
|
| compare_significant_contrasts |
Man page
Source code
|
| compare_surrogate_estimates |
Man page
Source code
|
| concatenate_runs |
Man page
Source code
|
| convert_counts |
Man page
Source code
|
| convert_gsc_ids |
Man page
Source code
|
| convert_ids |
Man page
Source code
|
| cordist |
Man page
Source code
|
| correlate_de_tables |
Man page
Source code
|
| count_clonotype_by_cluster |
Man page
Source code
|
| count_expt_snps |
Man page
Source code
|
| count_nmer |
Man page
Source code
|
| count_nmer,character-method |
Man page
|
| counts_from_surrogates |
Man page
Source code
|
| cp_options |
Man page
Source code
|
| create_expt |
Man page
Source code
|
| create_partitions |
Man page
Source code
|
| create_scd |
Man page
Source code
|
| create_se |
Man page
Source code
|
| de_venn |
Man page
Source code
|
| default_proper |
Man page
Source code
|
| deparse_go_value |
Man page
Source code
|
| deseq2_pairwise |
Man page
Source code
|
| deseq_lrt |
Man page
Source code
|
| deseq_pairwise |
Man page
Source code
|
| deseq_try_sv |
Man page
Source code
|
| disjunct_pvalues |
Man page
Source code
|
| dispatch_count_lines |
Man page
Source code
|
| dispatch_csv_search |
Man page
Source code
|
| dispatch_fasta_lengths |
Man page
Source code
|
| dispatch_filename_search |
Man page
Source code
|
| dispatch_gc |
Man page
Source code
|
| dispatch_metadata_extract |
Man page
Source code
|
| dispatch_metadata_ratio |
Man page
Source code
|
| dispatch_regex_search |
Man page
Source code
|
| divide_seq |
Man page
Source code
|
| do_batch |
Man page
Source code
|
| do_pairwise |
Man page
Source code
|
| do_topgo |
Man page
Source code
|
| download_gbk |
Man page
Source code
|
| download_microbesonline_files |
Man page
Source code
|
| dream_pairwise |
Man page
Source code
|
| ebseq_few |
Man page
Source code
|
| ebseq_pairwise |
Man page
Source code
|
| ebseq_pairwise_subset |
Man page
Source code
|
| ebseq_size_factors |
Man page
Source code
|
| ebseq_two |
Man page
Source code
|
| edger_pairwise |
Man page
Source code
|
| enrichResult-class |
Man page
|
| exclude_genes_expt |
Man page
Source code
|
| exprs,SummarizedExperiment-method |
Man page
|
| exprs,expt-method |
Man page
|
| exprs<-,ExpressionSet,data.frame-method |
Man page
|
| exprs<-,SummarizedExperiment,ANY-method |
Man page
|
| exprs<-,expt,ANY-method |
Man page
|
| expt |
Man page
Source code
|
| extract_abundant_genes |
Man page
Source code
|
| extract_coefficient_scatter |
Man page
Source code
|
| extract_de_plots |
Man page
Source code
|
| extract_go |
Man page
Source code
|
| extract_interesting_goseq |
Man page
Source code
|
| extract_keepers |
Man page
Source code
|
| extract_keepers,list,character-method |
Man page
|
| extract_lengths |
Man page
Source code
|
| extract_mayu_pps_fdr |
Man page
Source code
|
| extract_metadata |
Man page
Source code
|
| extract_msraw_data |
Man page
Source code
|
| extract_mzML_scans |
Man page
Source code
|
| extract_mzXML_scans |
Man page
Source code
|
| extract_peprophet_data |
Man page
Source code
|
| extract_pyprophet_data |
Man page
Source code
|
| extract_scan_data |
Man page
Source code
|
| extract_siggenes |
Man page
Source code
|
| extract_significant_genes |
Man page
Source code
|
| fData,SummarizedExperiment-method |
Man page
|
| fData,expt-method |
Man page
|
| fData<-,SummarizedExperiment,ANY-method |
Man page
|
| fData<-,expt,ANY-method |
Man page
|
| factor_rsquared |
Man page
Source code
|
| features_greater_than |
Man page
Source code
|
| features_in_single_condition |
Man page
Source code
|
| features_less_than |
Man page
Source code
|
| filter_counts |
Man page
Source code
|
| filter_scd |
Man page
Source code
|
| find_subseq_target_temp |
Man page
Source code
|
| find_working_dataset |
Man page
Source code
|
| find_working_mart |
Man page
Source code
|
| flanking_sequence |
Man page
Source code
|
| gather_cp_genes |
Man page
Source code
|
| gather_eupath_utrs_padding |
Man page
Source code
|
| gather_genes_orgdb |
Man page
Source code
|
| gather_masses |
Man page
Source code
|
| gather_ontology_genes |
Man page
Source code
|
| gather_preprocessing_metadata |
Man page
Source code
|
| gather_suppa_files |
Source code
|
| gather_utrs_padding |
Man page
Source code
|
| gather_utrs_txdb |
Man page
Source code
|
| genefilter_cv_counts |
Man page
Source code
|
| genefilter_kofa_counts |
Man page
Source code
|
| genefilter_pofa_counts |
Man page
Source code
|
| generate_expt_colors |
Man page
Source code
|
| generate_nn_groups |
Man page
Source code
|
| genomic_kmer_dist |
Man page
Source code
|
| genoplot_chromosome |
Man page
Source code
|
| getEdgeWeights |
Man page
Source code
|
| get_abundant_genes |
Man page
Source code
|
| get_backup_expression_data |
Man page
Source code
|
| get_backup_expression_data,ExpressionSet-method |
Man page
|
| get_backup_expression_data,SummarizedExperiment-method |
Man page
|
| get_biomart_example_gene |
Source code
|
| get_expt_colors |
Man page
Source code
|
| get_genesizes |
Man page
Source code
|
| get_git_commit |
Man page
Source code
|
| get_group_gsva_means |
Man page
Source code
|
| get_gsvadb_names |
Man page
Source code
|
| get_identifier |
Man page
Source code
|
| get_individual_snps |
Man page
Source code
|
| get_kegg_compounds |
Man page
Source code
|
| get_kegg_genes |
Man page
Source code
|
| get_kegg_orgn |
Man page
Source code
|
| get_kegg_sub |
Man page
Source code
|
| get_microbesonline_taxid |
Man page
Source code
|
| get_msigdb_metadata |
Man page
Source code
|
| get_num_den |
Source code
|
| get_pairwise_gene_abundances |
Man page
Source code
|
| get_plot_columns |
Man page
Source code
|
| get_proportion_snp_sets |
Man page
Source code
|
| get_res |
Man page
Source code
|
| get_sig_genes |
Man page
Source code
|
| get_sig_gsva_categories |
Man page
Source code
|
| get_snp_sets |
Source code
|
| get_vennerable_rows |
Source code
|
| get_yyyymm_commit |
Man page
Source code
|
| gff2gr |
Man page
Source code
|
| gff2irange |
Man page
Source code
|
| ggplotly_url |
Man page
Source code
|
| ggplt |
Man page
Source code
|
| godef |
Man page
Source code
|
| golev |
Man page
Source code
|
| golevel |
Man page
Source code
|
| golevel_df |
Man page
Source code
|
| goont |
Man page
Source code
|
| gosec |
Man page
Source code
|
| goseq2enrich |
Man page
Source code
|
| goseq_msigdb |
Man page
Source code
|
| goseq_table |
Man page
Source code
|
| goseq_trees |
Man page
Source code
|
| gostats2enrich |
Man page
Source code
|
| gostats_kegg |
Man page
Source code
|
| gostats_trees |
Man page
Source code
|
| gosyn |
Man page
Source code
|
| goterm |
Man page
Source code
|
| gotest |
Man page
Source code
|
| gprofiler2enrich |
Man page
Source code
Source code
|
| graph_metrics |
Man page
Source code
|
| group_mean_cds_length |
Man page
Source code
|
| guess_orgdb_keytype |
Man page
Source code
|
| heatmap.3 |
Man page
Source code
|
| hpgl_GOplot |
Man page
Source code
|
| hpgl_GroupDensity |
Man page
Source code
|
| hpgl_arescore |
Man page
Source code
|
| hpgl_cor |
Man page
Source code
|
| hpgl_dist |
Man page
Source code
|
| hpgl_filter_counts |
Man page
Source code
|
| hpgl_log2cpm |
Man page
Source code
|
| hpgl_norm |
Man page
Source code
|
| hpgl_padjust |
Man page
Source code
|
| hpgl_qshrink |
Man page
Source code
|
| hpgl_qstats |
Man page
Source code
|
| hpgl_rpkm |
Man page
Source code
|
| hpgl_topdiffgenes |
Source code
|
| hpgl_voom |
Man page
Source code
|
| hpgl_voomweighted |
Man page
Source code
|
| hpgltools |
Man page
|
| hpgltools-package |
Man page
|
| iDA |
Man page
|
| iDA,matrix-method |
Man page
|
| ihw_adjust |
Man page
Source code
|
| import_deseq |
Man page
Source code
|
| import_edger |
Man page
Source code
|
| impute_expt |
Man page
Source code
|
| init_xlsx |
Man page
Source code
|
| intersect_signatures |
Man page
Source code
|
| intersect_significant |
Man page
Source code
|
| kegg_vector_to_df |
Man page
Source code
|
| limma_pairwise |
Man page
Source code
|
| load_annotations |
Man page
Source code
|
| load_biomart_annotations |
Man page
Source code
|
| load_biomart_go |
Man page
Source code
|
| load_biomart_orthologs |
Man page
Source code
|
| load_genbank_annotations |
Man page
Source code
|
| load_gff_annotations |
Man page
Source code
|
| load_gmt_signatures |
Man page
Source code
|
| load_kegg_annotations |
Man page
Source code
|
| load_microbesonline_annotations |
Man page
|
| load_microbesonline_go |
Man page
|
| load_orgdb_annotations |
Man page
Source code
|
| load_orgdb_go |
Man page
Source code
|
| load_trinotate_annotations |
Man page
Source code
|
| load_trinotate_go |
Man page
Source code
|
| load_uniprot_annotations |
Man page
Source code
|
| load_uniprot_go |
Man page
Source code
|
| loadme |
Man page
Source code
|
| local_get_value |
Man page
Source code
|
| make_assembly_spec |
Man page
Source code
|
| make_bsgenome_from_fasta |
Source code
|
| make_dnaseq_spec |
Man page
Source code
|
| make_gsc_from_abundant |
Man page
Source code
|
| make_gsc_from_ids |
Man page
Source code
|
| make_gsc_from_pairwise |
Man page
Source code
|
| make_gsc_from_significant |
Source code
|
| make_id2gomap |
Man page
Source code
|
| make_kegg_df |
Man page
Source code
|
| make_limma_tables |
Man page
Source code
Source code
|
| make_pairwise_contrasts |
Man page
Source code
|
| make_pombe_expt |
Man page
Source code
|
| make_pombe_se |
Man page
Source code
|
| make_rnaseq_multibioproject |
Source code
|
| make_rnaseq_spec |
Man page
Source code
|
| make_simplified_contrast_matrix |
Man page
Source code
|
| make_tx_gene_map |
Man page
Source code
|
| map_keepers |
Man page
Source code
|
| map_kegg_dbs |
Man page
Source code
|
| map_orgdb_ids |
Man page
Source code
|
| mean_by_bioreplicate |
Man page
Source code
|
| mean_by_factor |
Man page
Source code
|
| median_by_factor |
Man page
Source code
|
| merge_gff_children |
Source code
|
| mesg |
Man page
Source code
|
| model_test |
Man page
Source code
|
| my_identifyAUBlocks |
Man page
|
| my_isva |
Man page
Source code
|
| my_runsims |
Man page
|
| mygetKGMLurl |
Source code
|
| mymakeContrasts |
Man page
Source code
|
| myretrieveKGML |
Man page
Source code
|
| network_from_matrix |
Man page
Source code
|
| noiseq_pairwise |
Man page
Source code
|
| normalize |
Man page
Source code
|
| normalize_counts |
Man page
Source code
|
| normalize_expt |
Man page
Source code
|
| normalize_se |
Man page
Source code
|
| notes,expt-method |
Man page
|
| orgdb_from_ah |
Man page
Source code
|
| overlap_geneids |
Man page
Source code
|
| overlap_groups |
Man page
Source code
|
| pData,SummarizedExperiment-method |
Man page
|
| pData,expt-method |
Man page
|
| pData<-,SummarizedExperiment,ANY-method |
Man page
|
| pData<-,expt,ANY-method |
Man page
|
| parse_msigdb |
Man page
Source code
|
| parse_msigdb_sqlite |
Man page
Source code
|
| parse_msigdb_xml |
Man page
Source code
|
| pattern_count_genome |
Man page
Source code
|
| pca_highscores |
Man page
Source code
|
| pca_information |
Man page
Source code
|
| pct_all_kegg |
Man page
Source code
|
| pct_kegg_diff |
Man page
Source code
|
| please_install |
Man page
Source code
|
| plot_3d_pca |
Man page
Source code
|
| plot_batchsv |
Man page
Source code
|
| plot_bcv |
Man page
Source code
|
| plot_boxplot |
Man page
Source code
|
| plot_cleaved |
Man page
Source code
|
| plot_corheat |
Man page
Source code
|
| plot_de_pvals |
Man page
Source code
|
| plot_density |
Man page
Source code
|
| plot_disheat |
Man page
Source code
|
| plot_dist_scatter |
Man page
Source code
|
| plot_enrichresult |
Man page
Source code
|
| plot_epitrochoid |
Man page
Source code
|
| plot_essentiality |
Man page
Source code
|
| plot_fun_venn |
Man page
Source code
|
| plot_goseq_pval |
Man page
Source code
|
| plot_gostats_pval |
Man page
Source code
|
| plot_gprofiler2_pval |
Man page
Source code
|
| plot_gprofiler_pval |
Man page
Source code
|
| plot_heatmap |
Man page
Source code
|
| plot_heatmap,ExpressionSet-method |
Man page
|
| plot_heatmap,SummarizedExperiment-method |
Man page
|
| plot_heatmap,data.frame-method |
Man page
|
| plot_heatmap,expt-method |
Man page
|
| plot_heatplus |
Man page
Source code
|
| plot_histogram |
Man page
Source code
|
| plot_hypotrochoid |
Man page
Source code
|
| plot_intensity_mz |
Man page
Source code
|
| plot_legend |
Man page
Source code
|
| plot_libsize |
Man page
Source code
|
| plot_libsize,ExpressionSet,ANY,ANY-method |
Man page
|
| plot_libsize,SummarizedExperiment,ANY,ANY-method |
Man page
|
| plot_libsize,data.frame,factor,character-method |
Man page
|
| plot_libsize,expt,ANY,ANY-method |
Man page
|
| plot_libsize_prepost |
Man page
Source code
|
| plot_linear_scatter |
Man page
Source code
|
| plot_ly |
Man page
|
| plot_ma_condition_de |
Source code
|
| plot_ma_de |
Man page
Source code
|
| plot_meta_interactive_sankey |
Source code
|
| plot_meta_sankey |
Man page
Source code
|
| plot_meta_sankey,expt-method |
Man page
|
| plot_multihistogram |
Man page
Source code
|
| plot_multiplot |
Man page
Source code
|
| plot_mzxml_boxplot |
Man page
Source code
|
| plot_nonzero |
Man page
Source code
|
| plot_nonzero,ExpressionSet-method |
Man page
|
| plot_nonzero,SummarizedExperiment-method |
Man page
|
| plot_nonzero,expt-method |
Man page
|
| plot_num_siggenes |
Man page
Source code
|
| plot_ontpval |
Man page
Source code
|
| plot_pairwise_ma |
Man page
Source code
|
| plot_pca |
Man page
Source code
|
| plot_pca_genes |
Man page
Source code
|
| plot_pcfactor |
Man page
Source code
|
| plot_pcload |
Man page
Source code
|
| plot_pcs |
Man page
Source code
|
| plot_pct_kept |
Man page
Source code
|
| plot_peprophet_data |
Man page
Source code
|
| plot_pyprophet_counts |
Man page
Source code
|
| plot_pyprophet_distribution |
Man page
Source code
|
| plot_pyprophet_points |
Man page
Source code
|
| plot_pyprophet_protein |
Man page
Source code
|
| plot_pyprophet_xy |
Man page
Source code
|
| plot_qq_all |
Man page
Source code
|
| plot_rmats |
Man page
Source code
|
| plot_rpm |
Man page
Source code
|
| plot_sample_bars |
Man page
Source code
|
| plot_sample_cvheatmap |
Man page
Source code
|
| plot_sample_heatmap |
Man page
Source code
|
| plot_sample_heatmap,ExpressionSet-method |
Man page
|
| plot_sample_heatmap,SummarizedExperiment-method |
Man page
|
| plot_sample_heatmap,expt-method |
Man page
|
| plot_sankey_de |
Man page
Source code
|
| plot_scatter |
Man page
Source code
|
| plot_seurat_scatter |
Man page
Source code
|
| plot_significant_bar |
Man page
Source code
|
| plot_single_qq |
Man page
Source code
|
| plot_sm |
Man page
Source code
|
| plot_sm,ExpressionSet-method |
Man page
|
| plot_sm,SummarizedExperiment-method |
Man page
|
| plot_sm,data.frame-method |
Man page
|
| plot_sm,expt-method |
Man page
|
| plot_spirograph |
Man page
Source code
|
| plot_suppa |
Man page
Source code
|
| plot_svfactor |
Man page
Source code
|
| plot_topgo_densities |
Man page
Source code
|
| plot_topgo_pval |
Man page
Source code
|
| plot_topn |
Man page
Source code
|
| plot_tsne |
Man page
Source code
|
| plot_variance_coefficients |
Man page
Source code
|
| plot_variance_coefficients,ExpressionSet-method |
Man page
|
| plot_variance_coefficients,SummarizedExperiment-method |
Man page
|
| plot_variance_coefficients,expt-method |
Man page
|
| plot_volcano_condition_de |
Man page
Source code
|
| plot_volcano_de |
Man page
Source code
|
| plotly_pca |
Man page
Source code
|
| pp |
Man page
Source code
|
| primer_qc |
Man page
Source code
|
| print.abundant_genes |
Man page
Source code
|
| print.all_gprofiler |
Man page
Source code
|
| print.all_pairwise |
Man page
Source code
|
| print.annotations_biomart |
Man page
Source code
|
| print.aucc_info |
Man page
Source code
|
| print.biomart_go |
Man page
Source code
|
| print.cds_variant_primers |
Man page
Source code
|
| print.classified_mutations |
Man page
Source code
|
| print.classifier_evaluation |
Man page
Source code
|
| print.clusterprofiler_result |
Man page
Source code
|
| print.combined_de |
Man page
Source code
|
| print.combined_table |
Man page
Source code
|
| print.correlation_heatmap |
Man page
Source code
|
| print.cross_table_comparison |
Man page
Source code
|
| print.density_plot |
Man page
Source code
|
| print.density_primers |
Man page
Source code
|
| print.deseq_lrt |
Man page
Source code
|
| print.distance_heatmap |
Man page
Source code
|
| print.expt |
Man page
Source code
|
| print.goseq_result |
Man page
Source code
|
| print.gostats_result |
Man page
Source code
|
| print.gprofiler_result |
Man page
Source code
|
| print.graphed_metrics |
Man page
Source code
|
| print.gsva_result |
Man page
Source code
|
| print.gsva_sig |
Man page
Source code
|
| print.legend_plot |
Man page
Source code
|
| print.libsize_plot |
Man page
Source code
|
| print.mapped_keepers |
Man page
Source code
|
| print.meta_sankey |
Man page
Source code
|
| print.nonzero_plot |
Man page
Source code
|
| print.partitioned_data |
Man page
Source code
|
| print.pattern_counted |
Man page
Source code
|
| print.pca_result |
Man page
Source code
|
| print.prepost_filter |
Man page
Source code
|
| print.preprocessing_metadata |
Man page
Source code
|
| print.proper_estimate |
Man page
Source code
|
| print.reordered_varpart |
Man page
Source code
|
| print.sig_genes |
Man page
Source code
|
| print.sig_intersect |
Man page
Source code
|
| print.snp_intersections |
Man page
Source code
|
| print.snp_sets |
Man page
Source code
|
| print.snps_genes |
Man page
Source code
|
| print.standardmedian_plot |
Man page
Source code
|
| print.topgo_result |
Man page
Source code
|
| print.topn_plot |
Man page
Source code
|
| print.varcoef_plot |
Man page
Source code
|
| print.varpart |
Man page
Source code
|
| print.written_expt |
Man page
Source code
|
| print.written_xlsx |
Man page
Source code
|
| print_ups_downs |
Man page
Source code
|
| proportions_by_factors |
Man page
Source code
|
| prune_network |
Man page
Source code
|
| pull_git_commit |
Man page
Source code
|
| random_ontology |
Man page
Source code
|
| rank_order_scatter |
Man page
Source code
|
| rbind_summary_rows |
Man page
Source code
|
| read_counts_expt |
Man page
Source code
|
| read_metadata |
Man page
Source code
|
| read_snp_columns |
Man page
Source code
|
| read_thermo_xlsx |
Man page
Source code
|
| recolor_points |
Man page
Source code
|
| record_seurat_samples |
Man page
Source code
|
| rename_vennerable_intersections |
Source code
|
| renderme |
Man page
Source code
|
| replot_varpart_percent |
Man page
Source code
|
| rex |
Man page
Source code
|
| rowData,ExpressionSet-method |
Man page
|
| rowData,expt-method |
Man page
|
| rowData<-,expt-method |
Man page
|
| rowMeans |
Man page
|
| rowmax_filter_counts |
Man page
Source code
|
| s2s_all_filters |
Man page
Source code
|
| sampleNames,SummarizedExperiment-method |
Man page
|
| sampleNames,expt-method |
Man page
|
| sampleNames<-,SummarizedExperiment,ANY-method |
Man page
|
| sampleNames<-,expt,ANY-method |
Man page
|
| sanitize_expt |
Man page
Source code
|
| sanitize_expt_fData |
Man page
Source code
|
| sanitize_expt_pData |
Man page
Source code
|
| sanitize_metadata |
Man page
Source code
|
| sanitize_number_encoding |
Man page
Source code
|
| sanitize_percent |
Man page
Source code
|
| saveme |
Man page
Source code
|
| score_amino_acids |
Source code
|
| score_gsva_likelihoods |
Man page
Source code
|
| score_mhess |
Man page
Source code
|
| self_evaluate_model |
Man page
Source code
|
| semantic_copynumber_extract |
Man page
Source code
|
| semantic_copynumber_filter |
Man page
Source code
|
| semantic_expt_filter |
Man page
Source code
|
| sequence_attributes |
Man page
Source code
|
| sequential_variants |
Man page
Source code
|
| set_expt_batches |
Man page
Source code
|
| set_expt_colors |
Man page
Source code
|
| set_expt_conditions |
Man page
Source code
|
| set_expt_factors |
Man page
Source code
|
| set_expt_genename_column |
Man page
Source code
|
| set_expt_genenames |
Man page
Source code
|
| set_expt_samplenames |
Man page
Source code
|
| shiny |
Man page
|
| sig_ontologies |
Man page
Source code
|
| significant_barplots |
Man page
Source code
|
| sillydist |
Man page
Source code
|
| simple_clusterprofiler |
Man page
Source code
|
| simple_cp_enricher |
Man page
Source code
|
| simple_dorothea |
Man page
Source code
|
| simple_filter_counts |
Man page
Source code
|
| simple_gadem |
Man page
Source code
|
| simple_goseq |
Man page
Source code
|
| simple_gostats |
Man page
Source code
|
| simple_gprofiler |
Man page
Source code
|
| simple_gprofiler2 |
Man page
Source code
|
| simple_gprofiler_old |
Man page
Source code
|
| simple_gsva |
Man page
Source code
|
| simple_motifRG |
Man page
Source code
|
| simple_pathview |
Man page
Source code
|
| simple_proper |
Man page
Source code
|
| simple_topgo |
Man page
Source code
|
| simple_topgo,character-method |
Man page
|
| simple_varpart |
Man page
Source code
|
| simple_xcell |
Man page
Source code
|
| single_topgo_tree |
Man page
Source code
|
| skim_seurat_metadata |
Man page
Source code
|
| slide_de_threshold |
Man page
Source code
|
| sm |
Man page
Source code
|
| snp_by_chr |
Man page
Source code
|
| snp_cds_primers |
Man page
Source code
|
| snp_density_primers |
Man page
Source code
|
| snp_subset_genes |
Man page
Source code
|
| snpnames2gr |
Man page
Source code
|
| snps_intersections |
Man page
Source code
|
| snps_vs_genes |
Man page
Source code
|
| snps_vs_genes_padded |
Man page
Source code
|
| state |
Man page
Source code
|
| state,SummarizedExperiment-method |
Man page
|
| state,expt-method |
Man page
|
| state<- |
Man page
|
| state<-,SummarizedExperiment-method |
Man page
|
| state<-,expt-method |
Man page
|
| steal_salmon_tx_ids |
Man page
Source code
|
| subset_expt |
Man page
Source code
|
| subset_expt,SummarizedExperiment-method |
Man page
|
| subset_genes |
Man page
Source code
|
| subset_ontology_search |
Man page
Source code
|
| subset_pyprophet_data |
Source code
|
| subset_se |
Source code
|
| subtract_expt |
Man page
Source code
|
| sum_eupath_exon_counts |
Man page
Source code
|
| sum_exon_widths |
Man page
Source code
|
| summarize_combined |
Source code
|
| summarize_scd_clusters |
Man page
Source code
|
| summarize_ups_downs |
Man page
Source code
|
| sva_modify_pvalues |
Man page
Source code
|
| synchronize_expt |
Man page
Source code
|
| table_style |
Man page
|
| tar_meta_column |
Man page
Source code
|
| tempfile |
Man page
Source code
|
| tmpmd5file |
Man page
Source code
|
| tnseq_multi_saturation |
Man page
Source code
|
| tnseq_saturation |
Man page
Source code
|
| topDiffGenes |
Man page
Source code
|
| topgo2enrich |
Man page
Source code
|
| topgo_tables |
Man page
Source code
|
| topgo_trees |
Man page
Source code
|
| transform_counts |
Man page
Source code
|
| u_plot |
Man page
Source code
|
| unAsIs |
Man page
Source code
|
| upsetr_combined_de |
Man page
Source code
|
| upsetr_sig |
Man page
Source code
|
| variance_expt |
Man page
Source code
|
| varpart_summaries |
Man page
Source code
|
| verbose |
Man page
|
| wgcna_network |
Man page
Source code
|
| what_happened |
Man page
Source code
|
| write_basic |
Man page
Source code
|
| write_cds_entries |
Man page
Source code
|
| write_classifier_summary |
Man page
Source code
|
| write_combined_legend |
Man page
Source code
|
| write_combined_summary |
Man page
Source code
|
| write_cp_data |
Man page
Source code
|
| write_de_table |
Man page
Source code
|
| write_density_primers |
Man page
Source code
|
| write_deseq |
Man page
Source code
|
| write_edger |
Man page
Source code
|
| write_expt |
Man page
Source code
|
| write_go_xls |
Man page
Source code
|
| write_goseq_data |
Man page
Source code
|
| write_gostats_data |
Man page
Source code
|
| write_gprofiler_data |
Man page
Source code
|
| write_gsva |
Man page
Source code
|
| write_limma |
Man page
Source code
Source code
|
| write_plots_de_xlsx |
Source code
|
| write_sample_design |
Man page
Source code
|
| write_sig_legend |
Man page
Source code
|
| write_snps |
Man page
Source code
|
| write_subset_ontologies |
Man page
Source code
|
| write_suppa_table |
Man page
Source code
|
| write_topgo_data |
Man page
Source code
|
| write_venns_de_xlsx |
Source code
|
| write_xlsx |
Man page
Source code
|
| write_xlsx,ANY,ANY,ANY,written_xlsx-method |
Man page
|
| xlsx_insert_png |
Man page
Source code
|
| xref_regions |
Man page
Source code
|
| ymxb_print |
Man page
Source code
|
