Man pages for eilslabs/epic
Integrative Analysis and Visualization of Epigenomic Sequencing Data
| annotate_to_gene_models | Annotate to gene models |
| annotate_to_genomic_features | Annotate to genomic features |
| available_gencode_fields | Returns all supported fields in GTF data |
| basic_genomic_regions_stat | Basic statistics on genomic regions |
| binary_search | Find intervals by binary search |
| bp | Mark the numbers to be number of base pairs |
| chipseq_hooks | Hook functions to extract ChIP-Seq peak data |
| chromatin_states_transition_chord_diagram | Chord diagram for chromatin states transistion |
| common_regions | Find common genomic regions across several samples |
| cor_columns | Number of columns which are highly correlated to other... |
| correlated_regions | Correlation between methylation and expression |
| cr_add_subtype_specificity | Add subtype specificity columns in cr |
| cr_enriched_at_tss | Enrichment of cr around tss |
| cr_gviz | Customized Gviz plot for a gene model |
| cr_hilbert | Hilbert curve visualization of correlated regions |
| cr_overlap_to_genomic_features | Enrichment of cr to other genomic features |
| cr_scatterplot_me | Scatter plot between methylation and expression in a... |
| enriched_heatmap_list_on_gene | Enriched heatmaps to visualize how signals are enriched at... |
| enriched_heatmap_list_on_genomic_features | Enriched heatmaps to visualize how signals are enriched at a... |
| enriched_heatmap_list_on_tss_cgi | Enriched heatmaps to visualize how signals are at enriched... |
| epic | Run pre-defiend scripts |
| extract_field_from_gencode | Extract field from gencode GTF file |
| extract_sites | Extract subset of sites in a set of intervals |
| filter_correlated_regions | Get correlated regions with significant correlations |
| find_neighbours | Find neighbour regions |
| genomic_corr_absdist | Absolute distance between two sets of genomic regions |
| genomic_corr_jaccard | Jaccard coefficient between two sets of genomic regions |
| genomic_corr_nintersect | Intersections between two sets of genomic regions |
| genomic_corr_pintersect | Intersection between two sets of genomic regions |
| genomic_corr_reldist | Relative distance between two sets of genomic regions |
| genomic_corr_sintersect | Intersection between two sets of genomic regions |
| genomic_regions_correlation | Correlation between two sets of genomic regions |
| get_mean_methylation_in_genomic_features | Calculate mean methylation value in a list of genomic... |
| get_peak_list | Get a list of peak regions |
| global_methylation_distribution | Global methylation distribution |
| heatmap_diff_methylation_in_genomic_features | Heatmap for differential methylation in genomic features |
| kb | Mark that the numbers represent number of kilo bases |
| load_config | Load and validate configuration file |
| logical_segment | Segmentation by a logical vector |
| make_transition_matrix_from_chromHMM | Generate transition matrix from chromHMM results |
| mb | Mark that the numbers represent number of mega bases |
| methylation_hooks | Hook functions to extract methylation data |
| methylation_subtype_classfication | Classify subtypes by methylation data |
| percentOverlaps | Find overlapping genomic regions |
| plot_coverage_and_methylation_on_genome | Plot coverage and methylation for a single sample |
| plot_multiple_samples_methylation_on_genome | Plot methylation for multiple samples |
| plot_subgroup_specificity_heatmap | Heatmap for visualizing subgroup specific genomic regions |
| print.bp | Print bp class objects |
| reduce2 | Merge genomic regions |
| reduce_cr | Merge neighbouring cr regions |
| reduce_cr_gap_test | Test a proper gap value for cr merging |
| run_pipeline | run pipeline through qsub system |
| scatterplot_with_boxplot | Scatterplot with boxplots on both sides |
| set_counter | Set a counter which represents percent finished in a loop |
| subgroup_specific_genomic_regions | Find subgroup specific regions |
| systemdf | Wrapper of system calls in which input and output are all... |
| wgbs_qcplot | Basic qc plot for bisulfite sequencing data |
