Man pages for rcavalcante/annotatr
Annotation of Genomic Regions to Genomic Annotations

annotate_regionsA function to intersect user region data with annotation data
annotationsexample_annotations data
annotatrannotatr: Annotation of Genomic Regions to Functional...
annotatr_cacheA global-variable to hold custom annotations loaded in an R...
build_ah_annotsA helper function to build arbitrary annotatinos from...
build_annotationsA function to build annotations from TxDb.* and AnnotationHub...
build_cpg_annotsA helper function to build CpG related annotations.
build_enhancer_annotsA helper function to build enhancer annotations for hg19 and...
build_gene_annotsA helper function to build genic annotations.
build_hmm_annotsA helper function to build chromHMM annotations for hg19 from...
build_lncrna_annotsA helper function to build lncRNA annotations.
builtin_annotationsFunction listing which annotations are available.
builtin_genomesFunction returning supported TxDb.* genomes
check_annotationsFunction to check for valid annotations
expand_annotationsFunction to expand annotation shortcuts
get_cellline_from_codeFunction to return cell line from chromatin annotation code
get_cellline_from_shortcutFunction to return cell line from chromatin annotation...
get_orgdb_nameFunction to get correct org.* package name based on genome
get_txdb_nameFunction to get correct TxDb.* package name based on genome
plot_annotationPlot the number of regions per annotation
plot_categoricalPlot a categorical data variable over another
plot_coannotationsPlot pair-wise annotations across regions
plot_numericalPlot numerical data over regions or regions summarized over...
plot_numerical_coannotationsPlot numerical data occurring in pairs of annotations
randomize_regionsRandomize Regions
read_annotationsRead custom annotations
read_regionsRead genomic regions in BEDX+Y format
reformat_hmm_codesFunction to recode classes from chromHMM type column
subset_order_tblFunction to subset a tbl_df or grouped_df by a column
summarize_annotationsSummarize annotation counts
summarize_categoricalSummarize categorical data over groupings of annotated...
summarize_numericalSummarize numerical data over groupings of annotated regions
tidy_annotationsFunction to tidy up annotation accessors for visualization
rcavalcante/annotatr documentation built on June 30, 2018, 4:10 p.m.