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| annotate_regions | A function to intersect user region data with annotation data |
| annotations | example_annotations data |
| annotatr | annotatr: Annotation of Genomic Regions to Functional Annotations |
| annotatr_cache | A global-variable to hold custom annotations loaded in an R session |
| build_ah_annots | A helper function to build arbitrary annotatinos from AnnotationHub |
| build_annotations | A function to build annotations from TxDb.* and AnnotationHub resources |
| build_cpg_annots | A helper function to build CpG related annotations. |
| build_enhancer_annots | A helper function to build enhancer annotations for hg19 and mm10 from FANTOM5. |
| build_gene_annots | A helper function to build genic annotations. |
| build_hmm_annots | A helper function to build chromHMM annotations for hg19 from UCSC Genome Browser. |
| build_lncrna_annots | A helper function to build lncRNA annotations. |
| builtin_annotations | Function listing which annotations are available. |
| builtin_genomes | Function returning supported TxDb.* genomes |
| check_annotations | Function to check for valid annotations |
| expand_annotations | Function to expand annotation shortcuts |
| get_cellline_from_code | Function to return cell line from chromatin annotation code |
| get_cellline_from_shortcut | Function to return cell line from chromatin annotation shortcut |
| get_orgdb_name | Function to get correct org.* package name based on genome |
| get_txdb_name | Function to get correct TxDb.* package name based on genome |
| plot_annotation | Plot the number of regions per annotation |
| plot_categorical | Plot a categorical data variable over another |
| plot_coannotations | Plot pair-wise annotations across regions |
| plot_numerical | Plot numerical data over regions or regions summarized over annotations |
| plot_numerical_coannotations | Plot numerical data occurring in pairs of annotations |
| randomize_regions | Randomize Regions |
| read_annotations | Read custom annotations |
| read_regions | Read genomic regions in BEDX+Y format |
| reformat_hmm_codes | Function to recode classes from chromHMM type column |
| subset_order_tbl | Function to subset a tbl_df or grouped_df by a column |
| summarize_annotations | Summarize annotation counts |
| summarize_categorical | Summarize categorical data over groupings of annotated regions |
| summarize_numerical | Summarize numerical data over groupings of annotated regions |
| tidy_annotations | Function to tidy up annotation accessors for visualization |