Files in RajLabMSSM/echoannot

echoverse module: Annotate fine-mapping results

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md NEWS.md R/CORCES2020_get_ATAC_peak_overlap.R R/CORCES2020_get_hichip_fithichip_overlap.R R/CORCES2020_prepare_bulkATAC_peak_overlap.R R/CORCES2020_prepare_scATAC_peak_overlap.R R/CORCES2020_scATAC_to_granges.R R/CS_bin_plot.R R/CS_counts_plot.R R/IMPACT_process.R R/IMPACT_query.R R/MOTIFBREAKR.R R/MOTIFBREAKR_calc_pvals.R R/MOTIFBREAKR_filter.R R/MOTIFBREAKR_filter_by_metadata.R R/MOTIFBREAKR_has_pvals.R R/MOTIFBREAKR_make_id.R R/MOTIFBREAKR_plot.R R/MOTIFBREAKR_summarize.R R/NOTT2019_epigenomic_histograms.R R/NOTT2019_get_epigenomic_peaks.R R/NOTT2019_get_epigenomic_peaks_macs2.R R/NOTT2019_get_interactions.R R/NOTT2019_get_interactome.R R/NOTT2019_get_promoter_celltypes.R R/NOTT2019_get_promoter_interactome_data.R R/NOTT2019_get_regulatory_regions.R R/NOTT2019_marker_key.R R/NOTT2019_plac_seq_plot.R R/NOTT2019_prepare_peak_overlap.R R/NOTT2019_prepare_placseq_overlap.R R/NOTT2019_prepare_regulatory_overlap.R R/NOTT2019_superenhancers.R R/PAINTOR_process.R R/ROADMAP_annotate.R R/ROADMAP_chromatin_states.R R/ROADMAP_construct_reference.R R/ROADMAP_merge_and_process.R R/ROADMAP_query.R R/ROADMAP_tabix.R R/XGR_enrichment.R R/XGR_enrichment_bootstrap.R R/XGR_enrichment_plot.R R/XGR_filter_assays.R R/XGR_filter_sources.R R/XGR_import_annotations.R R/XGR_iterate_enrichment.R R/XGR_iterate_overlap.R R/XGR_merge_and_process.R R/XGR_parse_metadata.R R/XGR_plot_enrichment.R R/XGR_prepare_foreground_background.R R/XGR_query.R R/XGR_sep_handler.R R/add_mb.R R/add_regulatory_rects.R R/add_track_lines.R R/add_xtext.R R/annotate_missense.R R/annotate_snps.R R/annotation_file_name.R R/as_ggbio.R R/as_ggplot.R R/as_patchwork.R R/as_tracks.R R/assay_color_dict.R R/biomart_snp_info.R R/biomart_snps_to_geneInfo.R R/cell_type_specificity.R R/check_bigwig_metadata.R R/check_grlist.R R/clean_granges.R R/coloc_nominated_eGenes.R R/convert_plots.R R/count_and_melt.R R/counts_summary.R R/create_finemap_track.R R/create_gwas_track.R R/data.R R/filter_chomatin_states.R R/find_top_consensus.R R/get_CORCES2020_bulkATACseq_peaks.R R/get_CORCES2020_cicero_coaccessibility.R R/get_CORCES2020_hichip_fithichip_loop_calls.R R/get_CORCES2020_scATACseq_celltype_peaks.R R/get_CORCES2020_scATACseq_peaks.R R/get_NOTT2019_interactome.R R/get_NOTT2019_superenhancer_interactome.R R/get_bbparam.R R/get_consensus_pos.R R/get_data.R R/get_lead_pos.R R/get_max_histogram_height.R R/get_top_consensus_pos.R R/get_window_limits.R R/get_zoom_xlims.R R/ggbio_to_mb.R R/granges_overlap.R R/haplor_epigenetic_enrichment.R R/haplor_epigenetics_summary.R R/haplor_haploreg.R R/haplor_regulomedb.R R/import_bigwig_filtered.R R/import_ucsc_bigwigs.R R/initialize_plac_seq_plot.R R/leadSNP_comparison.R R/limits_from_ggplot.R R/merge_celltype_specific_epigenomics.R R/message_parallel.R R/messager.R R/name_filter_convert.R R/order_loci.R R/palette_gnbu.R R/peak_overlap.R R/peak_overlap_plot.R R/plot_dataset_overlap.R R/plot_missense.R R/prepare_highlight_plac_data.R R/rbind_granges.R R/require_arg.R R/save_annotations.R R/select_genome.R R/snps_by_mutation_type.R R/standardize_celltypes.R R/super_summary_plot.R R/test_enrichment.R R/tracks_to_ggplot_list.R README.Rmd README.md inst/echoannot_0.99.1.pdf inst/hex/hexSticker.Rmd man/CORCES2020_get_ATAC_peak_overlap.Rd man/CORCES2020_get_hichip_fithichip_overlap.Rd man/CORCES2020_prepare_bulkATAC_peak_overlap.Rd man/CORCES2020_prepare_scATAC_peak_overlap.Rd man/CS_bin_plot.Rd man/CS_counts_plot.Rd man/IMPACT_files.Rd man/IMPACT_process.Rd man/IMPACT_query.Rd man/MOTIFBREAKR.Rd man/MOTIFBREAKR_calc_pvals.Rd man/MOTIFBREAKR_filter.Rd man/MOTIFBREAKR_filter_by_metadata.Rd man/MOTIFBREAKR_make_id.Rd man/MOTIFBREAKR_plot.Rd man/MOTIFBREAKR_summarize.Rd man/NOTT2019_bigwig_metadata.Rd man/NOTT2019_epigenomic_histograms.Rd man/NOTT2019_get_epigenomic_peaks.Rd man/NOTT2019_get_interactions.Rd man/NOTT2019_get_interactome.Rd man/NOTT2019_get_promoter_celltypes.Rd man/NOTT2019_get_promoter_interactome_data.Rd man/NOTT2019_get_regulatory_regions.Rd man/NOTT2019_plac_seq_plot.Rd man/NOTT2019_superenhancers.Rd man/PAINTOR_process.Rd man/ROADMAP_construct_reference.Rd man/ROADMAP_merge_and_process.Rd man/ROADMAP_query.Rd man/ROADMAP_tabix.Rd man/XGR_enrichment.Rd man/XGR_enrichment_bootstrap.Rd man/XGR_enrichment_plot.Rd man/XGR_filter_assays.Rd man/XGR_filter_sources.Rd man/XGR_import_annotations.Rd man/XGR_iterate_enrichment.Rd man/XGR_iterate_overlap.Rd man/XGR_merge_and_process.Rd man/XGR_parse_metadata.Rd man/XGR_plot_enrichment.Rd man/XGR_prepare_foreground_background.Rd man/XGR_sep_handler.Rd man/add_mb.Rd man/annotate_missense.Rd man/annotate_snps.Rd man/annotation_file_name.Rd man/biomart_snp_info.Rd man/biomart_snps_to_geneInfo.Rd man/cell_type_specificity.Rd man/clean_granges.Rd man/coloc_nominated_eGenes.Rd man/convert_plots.Rd man/filter_chromatin_states.Rd man/find_top_consensus.Rd man/get_CORCES2020_bulkATACseq_peaks.Rd man/get_CORCES2020_cicero_coaccessibility.Rd man/get_CORCES2020_hichip_fithichip_loop_calls.Rd man/get_CORCES2020_scATACseq_celltype_peaks.Rd man/get_CORCES2020_scATACseq_peaks.Rd man/get_NOTT2019_interactome.Rd man/get_NOTT2019_superenhancer_interactome.Rd man/get_bpparam.Rd man/get_data.Rd man/get_max_histogram_height.Rd man/get_top_consensus_pos.Rd man/get_window_limits.Rd man/granges_overlap.Rd man/haplor_epigenetics_enrichment.Rd man/haplor_epigenetics_summary.Rd man/haplor_haploreg.Rd man/haplor_regulomedb.Rd man/import_bigwig_filtered.Rd man/import_ucsc_bigwigs.Rd man/merge_celltype_specific_epigenomics.Rd man/message_parallel.Rd man/name_filter_convert.Rd man/order_loci.Rd man/peak_overlap.Rd man/peak_overlap_plot.Rd man/plot_dataset_overlap.Rd man/plot_missense.Rd man/rbind_granges.Rd man/select_genome.Rd man/snps_by_mutation_type.Rd man/super_summary_plot.Rd man/test_enrichment.Rd man/tracks_to_ggplot_list.Rd man/xgr_example.Rd man/xgr_query.Rd tests/testthat.R tests/testthat/Rplots.pdf tests/testthat/test-IMPACT_query.R tests/testthat/test-NOTT2019_epigenomic_histograms.R tests/testthat/test-NOTT2019_plac_seq_plot.R tests/testthat/test-ROADMAP_query.R tests/testthat/test-annotate_snps.R tests/testthat/test-convert_plots.R tests/testthat/test-granges_overlap.R tests/testthat/test-import_ucsc_bigwigs.R tests/testthat/test-motifbreakR.R tests/testthat/test-super_summary_plot.R tests/testthat/test-test_enrichment.R vignettes/cell_type_specific_epigenomics.Rmd vignettes/echoannot.Rmd