API for jokergoo/epik
Integrative Analysis and Visualization of Epigenomic Sequencing Data
| Global functions | |
|---|---|
| [.chromatin_states_transition_matrix | Man page |
| [.subgroup_specific_genomic_regions | Man page |
| add_boxplot_as_column_annotation | Source code |
| add_chord_diagram_legend | Source code |
| add_mean_methylation | Source code |
| add_transparency | Source code |
| annotate_to_gene_models | Man page Source code |
| annotate_to_genomic_features | Man page Source code |
| available_gencode_fields | Man page Source code |
| average_in_window | Source code |
| binary_search | Source code |
| bp | Man page Source code |
| cg_percent_per_window | Source code |
| chipseq_hooks | Man page Source code |
| chromatin_states_transition_chord_diagram | Man page Source code |
| common_regions | Man page Source code |
| compare_meth | Man page Source code |
| constructAnnotationTrack | Source code |
| cor_columns | Man page |
| correlated_regions | Man page Source code |
| correlated_regions_by_window | Man page Source code |
| cr_add_subtype_specificity | Man page Source code |
| cr_concatenate | Man page Source code |
| cr_coverage_on_genes | Man page Source code |
| cr_enriched_heatmap | Man page Source code |
| cr_enriched_heatmap_at_gene | Man page Source code |
| cr_enriched_heatmap_at_genomic_features | Man page Source code |
| cr_enriched_heatmap_at_tss | Man page Source code |
| cr_enriched_heatmap_at_tss_cgi | Man page Source code |
| cr_genes_function_enrichment | Source code |
| cr_genes_gtrellis | Man page Source code |
| cr_genic_stat | Man page Source code |
| cr_gviz | Man page Source code |
| cr_hilbert_curve | Man page Source code |
| cr_reduce | Man page Source code |
| cr_scatterplot | Man page Source code |
| diameter | Source code |
| dist_by_closeness | Source code |
| dist_by_closeness2 | Source code |
| do_david | Source code |
| enrich_with_histone_mark | Man page Source code |
| enrich_with_methylation | Man page Source code |
| extract_field_from_gencode | Man page Source code |
| extract_sites | Man page Source code |
| find_neighbours | Man page Source code |
| format_sample_id_and_subgroup | Source code |
| general_chipseq_association | Man page Source code |
| general_chipseq_association_to_methylation | Man page Source code |
| generate_background_from_methylation_features | Source code |
| generate_color_fun | Source code |
| generate_diff_color_fun | Source code |
| genomic_corr_absdist | Man page Source code |
| genomic_corr_intersect | Man page Source code |
| genomic_corr_jaccard | Man page Source code |
| genomic_corr_reldist | Man page Source code |
| genomic_regions_basic_stat | Man page Source code |
| genomic_regions_correlation | Man page Source code |
| getChromInfoFromUCSC | Source code |
| get_chipseq_association_stat | Source code |
| get_chromHMM_list | Man page Source code |
| get_mean_histone_density_in_genomic_features | Source code |
| get_mean_methylation_in_genomic_features | Man page Source code |
| get_peak_list | Man page Source code |
| get_sig_cr | Man page Source code |
| gp_c | Source code |
| heatmap_diff_methylation_in_genomic_features | Man page Source code |
| heatmap_subgroup_specificity | Man page Source code |
| hilbert_curve_chipseq_difference | Man page Source code |
| hilbert_curve_methylation_difference | Man page Source code |
| import_gencode_as_txdb | Man page Source code |
| initialize_project_directory | Man page Source code |
| is.file | Source code |
| is.not.null | Source code |
| kb | Man page Source code |
| load_epik_config | Man page Source code |
| make_ecdf | Source code |
| make_transition_matrix_from_chromHMM | Man page Source code |
| make_upset | Source code |
| mat_dist | Man page Source code |
| match_by_gencode | Man page Source code |
| max_reduce_of_significance | Source code |
| mb | Man page Source code |
| mean_chromHMM_overlap | Source code |
| mean_overlap | Source code |
| merge_cpg_dinucleotide_methylation | Man page Source code |
| merge_row_order | Source code |
| methylation_global_distribution | Man page Source code |
| methylation_gtrellis | Man page Source code |
| methylation_gtrellis_multiple_samples | Man page Source code |
| methylation_hooks | Man page Source code |
| methylation_qcplot | Man page Source code |
| normalize_epigenomic_signals | Source code |
| overlap_mean_signals | Source code |
| percentOverlaps | Man page Source code |
| plot_upset | Source code |
| print.bp | Man page Source code |
| print.chromatin_states_transition_matrix | Man page Source code |
| print.methylation_hooks | Man page Source code |
| print.subgroup_specific_genomic_regions | Man page Source code |
| pushTrackList | Source code |
| qq_message | Source code |
| qq_stop | Source code |
| qq_warning | Source code |
| read.chromInfo | Source code |
| readRDS_or_readRData | Source code |
| reduce2 | Man page Source code |
| reduce_cr_by_gene | Source code |
| reduce_david_results | Man page Source code |
| register_global_var | Man page Source code |
| return2 | Source code |
| rowWhichMax | Source code |
| scatterplot_with_boxplot | Man page Source code |
| set_chr | Source code |
| set_counter | Man page Source code |
| set_proper_seqlengths | Source code |
| sig_cr_compare_cutoff | Man page Source code |
| sig_cr_enriched_heatmap | Man page Source code |
| sig_cr_heatmap | Man page Source code |
| sig_cytoband_gtrellis | Man page Source code |
| state_names | Man page Source code |
| state_names<- | Man page |
| strwrap2 | Source code |
| subgroup_specific_genomic_regions | Man page Source code |
| submit_to_david | Man page Source code |
| systemdf | Man page Source code |
| t.chromatin_states_transition_matrix | Man page Source code |
| weighted_mean | Source code |
