Man pages for jokergoo/epik
Integrative Analysis and Visualization of Epigenomic Sequencing Data
| annotate_to_gene_models | Annotate genomic regions to gene models |
| annotate_to_genomic_features | Annotate genomic regions to a list of genomic features |
| available_gencode_fields | Returns all supported fields in GTF file |
| bp | Add unit "bp" to the number |
| chipseq_hooks | Read ChIP-Seq dataset |
| chromatin_states_transition_chord_diagram | Chord diagram for visualizing chromatin states transitions |
| common_regions | Find common genomic regions across samples |
| compare_meth | Compare raw and smoothed methylation |
| cor_columns | Number of columns which are highly correlated to other... |
| correlated_regions | Correlation between methylation and expression |
| correlated_regions_by_window | Correlated regions in a specified region |
| cr_add_subtype_specificity | Add subtype specificity columns in CR |
| cr_concatenate | Concatenate CR objects |
| cr_coverage_on_genes | CR coverage on genes |
| cr_enriched_heatmap | Visualize landscape of genome-wide correlations |
| cr_enriched_heatmap_at_gene | Visualizing enrichment for epigenomic signals at gene body |
| cr_enriched_heatmap_at_genomic_features | Visualizing enrichment for epigenomic signals at TSS-CGIs |
| cr_enriched_heatmap_at_tss | Visualizing enrichment for epigenomic signals at TSS |
| cr_enriched_heatmap_at_tss_cgi | Visualizing enrichment for epigenomic signals at TSS-CGIs |
| cr_genes_gtrellis | Visualize CR genes in gtrellis layout |
| cr_genic_stat | Plot general statistics for the annotations to genes |
| cr_gviz | Customized Gviz plot for a single gene |
| cr_hilbert_curve | Visualize global correlation by Hilbert curve |
| cr_reduce | Merge correlated regions |
| cr_scatterplot | Scatter plot between methylation and expression in one... |
| enrich_with_histone_mark | Normalize histone modification signals to target regions |
| enrich_with_methylation | Normalize methylation to target regions |
| Extract.chromatin_states_transition_matrix | Subset chromatin_states_transition_matrix class object |
| extract_field_from_gencode | Extract field from gencode GTF file |
| extract_sites | Extract subset of sites in a set of intervals |
| Extract.subgroup_specific_genomic_regions | Subset the subgroup_specific_genomic_regions class object |
| find_neighbours | Find neighbour regions |
| general_chipseq_association | General association between histone modifications |
| general_chipseq_association_to_methylation | General association between histone modifications and... |
| genomic_corr_absdist | Absolute distance between two sets of genomic regions |
| genomic_corr_intersect | Intersections between two sets of genomic regions |
| genomic_corr_jaccard | Jaccard coefficient between two sets of genomic regions |
| genomic_corr_reldist | Relative distance between two sets of genomic regions |
| genomic_regions_basic_stat | Visualize basic statistics on genomic regions |
| genomic_regions_correlation | Correlation between two sets of genomic regions |
| get_chromHMM_list | Get a list of chromatin segmentation regions |
| get_mean_methylation_in_genomic_features | Calculate mean methylation in a list of genomic features |
| get_peak_list | Get a list of peak regions for a given histone mark |
| get_sig_cr | Get significant CRs |
| heatmap_diff_methylation_in_genomic_features | Heatmap for differential methylated genomic features |
| heatmap_subgroup_specificity | Heatmap for visualizing subgroup specific genomic regions |
| hilbert_curve_chipseq_difference | Visualize ChIP-Seq signal difference by Hilbert curve |
| hilbert_curve_methylation_difference | Visualize methylation difference by Hilbert curve |
| import_gencode_as_txdb | Import gencode GTF file as a TxDb object |
| initialize_project_directory | Initialize project directories |
| kb | Add unit "kb" to the number |
| load_epik_config | Load and validate configuration file |
| make_transition_matrix_from_chromHMM | Generate transition matrix from chromHMM results |
| match_by_gencode | Filter one GTF annotation by another |
| mat_dist | Visualize distribution of a matrix or a list |
| mb | Add unit "mb" to the number |
| merge_cpg_dinucleotide_methylation | Merge methylation for CpG dinucleotide |
| methylation_global_distribution | Global methylation distribution |
| methylation_gtrellis | Plot coverage and methylation for a single sample |
| methylation_gtrellis_multiple_samples | Plot methylation for multiple samples as heatmaps |
| methylation_hooks | Read methylation dataset |
| methylation_qcplot | Basic qc plot for distribution of methylation and CpG... |
| percentOverlaps | Overlap genomic regions |
| print.bp | Print the bp object |
| print.chromatin_states_transition_matrix | Print chromatin_states_transition_matrix class object |
| print.methylation_hooks | Print the methylation_hooks object |
| print.subgroup_specific_genomic_regions | Print subgroup_specific_genomic_regions class object |
| reduce2 | Merge genomic regions |
| reduce_david_results | reduce david results |
| register_global_var | Register global variables |
| scatterplot_with_boxplot | Scatterplot with boxplots on both sides |
| set_counter | Set a counter which represents the percentage finished in a... |
| sig_cr_compare_cutoff | Compare cutoff for determining significant correlated regions |
| sig_cr_enriched_heatmap | Visualize significantly correlated regions |
| sig_cr_heatmap | Heatmaps for significant correlated regions |
| sig_cytoband_gtrellis | Visualize correlations in cytoband |
| state_names | Simply return names of chromatin states |
| state_namesAssign | Change chromatin state names |
| subgroup_specific_genomic_regions | Find subgroup specific regions |
| submit_to_david | Doing DAVID analysis |
| systemdf | Wrapper of system calls in which input and output are all... |
| t.chromatin_states_transition_matrix | Transpose the chromatin transition matrix |
