API for RajLabMSSM/echoannot
echoverse module: Annotate fine-mapping results
| Global functions | |
|---|---|
| CORCES2020_get_ATAC_peak_overlap | Man page Source code |
| CORCES2020_get_HiChIP_FitHiChIP_overlap | Source code |
| CORCES2020_get_hichip_fithichip_overlap | Man page Source code |
| CORCES2020_prepare_bulkATAC_peak_overlap | Man page Source code |
| CORCES2020_prepare_scATAC_peak_overlap | Man page Source code |
| CORCES2020_scATAC_to_granges | Source code |
| CS_bin_plot | Man page Source code |
| CS_counts_plot | Man page Source code |
| IMPACT_files | Man page |
| IMPACT_process | Man page Source code |
| IMPACT_query | Man page Source code |
| MOTIFBREAKR | Man page Source code |
| MOTIFBREAKR_calc_pvals | Man page Source code |
| MOTIFBREAKR_filter | Man page Source code |
| MOTIFBREAKR_filter_by_metadata | Man page Source code |
| MOTIFBREAKR_has_pvals | Source code |
| MOTIFBREAKR_make_id | Man page Source code |
| MOTIFBREAKR_plot | Man page Source code |
| MOTIFBREAKR_summarize | Man page Source code |
| NOTT2019_bigwig_metadata | Man page |
| NOTT2019_epigenomic_histograms | Man page Source code |
| NOTT2019_get_epigenomic_peaks | Man page Source code |
| NOTT2019_get_interactions | Man page Source code |
| NOTT2019_get_interactome | Man page Source code |
| NOTT2019_get_promoter_celltypes | Man page Source code |
| NOTT2019_get_promoter_interactome_data | Man page Source code |
| NOTT2019_get_regulatory_regions | Man page Source code |
| NOTT2019_marker_key | Source code |
| NOTT2019_plac_seq_plot | Man page Source code |
| NOTT2019_prepare_peak_overlap | Source code |
| NOTT2019_prepare_placseq_overlap | Source code |
| NOTT2019_prepare_regulatory_overlap | Source code |
| NOTT2019_superenhancers | Man page Source code |
| PAINTOR_process | Man page Source code |
| ROADMAP_annotate | Source code |
| ROADMAP_chromatin_states | Source code |
| ROADMAP_construct_reference | Man page Source code |
| ROADMAP_merge_and_process | Man page Source code |
| ROADMAP_query | Man page Source code |
| ROADMAP_tabix | Man page Source code |
| XGR_enrichment | Man page Source code |
| XGR_enrichment_bootstrap | Man page Source code |
| XGR_enrichment_plot | Man page Source code |
| XGR_filter_assays | Man page Source code |
| XGR_filter_sources | Man page Source code |
| XGR_import_annotations | Man page Source code |
| XGR_iterate_enrichment | Man page Source code |
| XGR_iterate_overlap | Man page Source code |
| XGR_merge_and_process | Man page Source code |
| XGR_parse_metadata | Man page Source code |
| XGR_plot_enrichment | Man page Source code |
| XGR_prepare_foreground_background | Man page Source code |
| XGR_query | Man page Source code |
| XGR_sep_handler | Man page Source code |
| add_mb | Man page Source code |
| add_regulatory_rects | Source code |
| add_track_lines | Source code |
| add_xtext | Source code |
| annotate_missense | Man page Source code |
| annotate_snps | Man page Source code |
| annotation_file_name | Man page Source code |
| as_ggbio | Source code |
| as_ggplot | Source code |
| as_patchwork | Source code |
| as_tracks | Source code |
| assay_color_dict | Source code |
| biomart_snp_info | Man page Source code |
| biomart_snps_to_geneInfo | Man page Source code |
| cell_type_specificity | Man page Source code |
| check_bigwig_metadata | Source code |
| check_grlist | Source code |
| clean_granges | Man page Source code |
| coloc_nominated_egenes | Man page Source code |
| convert_plots | Man page Source code |
| count_and_melt | Source code |
| counts_summary | Source code |
| create_finemap_track | Source code |
| create_gwas_track | Source code |
| filter_chromatin_states | Man page Source code |
| find_top_consensus | Man page Source code |
| get_CORCES2020_HiChIP_FitHiChIP_loop_calls | Source code |
| get_CORCES2020_bulkATACseq_peaks | Man page Source code |
| get_CORCES2020_cicero_coaccessibility | Man page Source code |
| get_CORCES2020_hichip_fithichip_loop_calls | Man page Source code |
| get_CORCES2020_scATACseq_celltype_peaks | Man page Source code |
| get_CORCES2020_scATACseq_peaks | Man page Source code |
| get_NOTT2019_interactome | Man page Source code |
| get_NOTT2019_superenhancer_interactome | Man page Source code |
| get_bpparam | Man page Source code |
| get_consensus_pos | Source code |
| get_data | Man page Source code |
| get_lead_pos | Source code |
| get_max_histogram_height | Man page Source code |
| get_top_consensus_pos | Man page Source code |
| get_window_limits | Man page Source code |
| get_zoom_xlims | Source code |
| ggbio_to_mb | Source code |
| granges_overlap | Man page Source code |
| haplor_epigenetics_enrichment | Man page Source code |
| haplor_epigenetics_summary | Man page Source code |
| haplor_haploreg | Man page Source code |
| haplor_regulomedb | Man page Source code |
| import_bigwig_filtered | Man page Source code |
| import_ucsc_bigwigs | Man page Source code |
| initialize_plac_seq_plot | Source code |
| leadSNP_comparison | Source code |
| limits_from_ggplot | Source code |
| merge_celltype_specific_epigenomics | Man page Source code |
| message_parallel | Man page Source code |
| messager | Source code |
| name_filter_convert | Man page Source code |
| order_loci | Man page Source code |
| palette_gnbu | Source code |
| peak_overlap | Man page Source code |
| peak_overlap_plot | Man page Source code |
| plot_dataset_overlap | Man page Source code |
| plot_missense | Man page Source code |
| prepare_highlight_plac_data | Source code |
| rbind_granges | Man page Source code |
| require_arg | Source code |
| save_annotations | Source code |
| select_genome | Man page Source code |
| snps_by_mutation_type | Man page Source code |
| standardize_celltypes | Source code |
| super_summary_plot | Man page Source code |
| test_enrichment | Man page Source code |
| tracks_to_ggplot_list | Man page Source code |
| xgr_example | Man page |
