Function reference • echoannot

All functions
`CORCES2020_get_ATAC_peak_overlap()`	Get overlap between datatable of SNPs and scATAC peaks
`CORCES2020_get_hichip_fithichip_overlap()`	Get overlap between data table of SNPs and HiChIP_FitHiChIP coaccessibility anchors
`CS_bin_plot()`	Plot CS bin counts
`CS_counts_plot()`	Bar plot of tool-specific CS sizes
`IMPACT_files`	IMPACT files
`IMPACT_query()`	Query IMPACT annotations
`MOTIFBREAKR()`	Run motifbreakR
`MOTIFBREAKR_calc_pvals()`	Calculate motifbreakR p-values
`MOTIFBREAKR_filter()`	Merge and filter motifbreakR + echolocatoR results
`MOTIFBREAKR_plot()`	Plot motifbreakR results
`MOTIFBREAKR_summarize()`	Summarize motifbreakR + echolocatoR results
`NOTT2019_bigwig_metadata`	Metadata and links to data
`NOTT2019_epigenomic_histograms()`	Plot brain cell-specific epigenomic data
`NOTT2019_get_epigenomic_peaks()`	Download cell type-specific epigenomic peaks
`NOTT2019_get_interactome()`	Import cell type-specific interactomes
`NOTT2019_get_promoter_interactome_data()`	Get cell type-specific promoter/emhancer/interactome data
`NOTT2019_get_regulatory_regions()`	Get regulatory regions: Nott2019
`NOTT2019_plac_seq_plot()`	Plot brain cell-specific interactome data
`ROADMAP_construct_reference()`	Gather Roadmap annotation metadata
`ROADMAP_query()`	Query Roadmap Query Roadmap annotations using a set of genomic coordinates.
`XGR_enrichment()`	XGR enrichment
`XGR_enrichment_bootstrap()`	XGR enrichment (bootstrapped)
`XGR_filter_assays()`	Filter assays
`XGR_filter_sources()`	Filter sources
`add_mb()`	Add Mb
`annotate_missense()`	Annotate any missense variants
`annotate_snps()`	Annotate merged fine-mapping results from all loci
`annotation_file_name()`	Annotation file name
`convert_plots()`	Convert plots to various formats
`get_CORCES2020_bulkATACseq_peaks()`	bulkATACseq peaks from human brain tissue
`get_CORCES2020_cicero_coaccessibility()`	Cicero_coaccessibility from human brain tissue
`get_CORCES2020_hichip_fithichip_loop_calls()`	FitHiChIP loop calls from human brain tissue
`get_CORCES2020_scATACseq_celltype_peaks()`	scATACseq cell type-specific peaks from human brain tissue
`get_CORCES2020_scATACseq_peaks()`	scATACseq peaks from human brain tissue
`get_NOTT2019_superenhancer_interactome()`	Brain cell type-specific interactomes with superenhancers
`get_window_limits()`	Get widow limits
`granges_overlap()`	Find GenomicRanges overlap Find overlap genomic position overlap between two GRanges objects.
`import_ucsc_bigwigs()`	Import bigwig files from the UCSC Genome Browser
`merge_celltype_specific_epigenomics()`	Merge all cell-type-specific epigenomics
`plot_dataset_overlap()`	Plot inter-study SNP overlap
`plot_missense()`	Plot any missense variants
`super_summary_plot()`	Merge all summary plots into one super plot
`test_enrichment()`	Test enrichment
`xgr_example`	Example XGR query
`XGR_query()`	Download, standardize, and merge XGR annotations

Reference

All functions