annotatr: Annotation of Genomic Regions to Genomic Annotations

Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("annotatr")
AuthorRaymond G. Cavalcante [aut, cre], Maureen A. Sartor [ths]
Bioconductor views Annotation FunctionalGenomics GenomeAnnotation Software Visualization
Date of publicationNone
MaintainerRaymond G. Cavalcante <rcavalca@umich.edu>
LicenseGPL-3
Version1.2.0

View on Bioconductor

Man pages

annotate_regions: A function to intersect user region data with annotation data

annotations: example_annotations data

annotatr: annotatr: Annotation of Genomic Regions to Functional...

annotatr_cache: A global-variable to hold custom annotations loaded in an R...

build_ah_annots: A helper function to build arbitrary annotatinos from...

build_annotations: A function to build annotations from TxDb.* and AnnotationHub...

build_cpg_annots: A helper function to build CpG related annotations.

build_enhancer_annots: A helper function to build enhancer annotations for hg19 and...

build_gene_annots: A helper function to build genic annotations.

build_hmm_annots: A helper function to build chromHMM annotations for hg19 from...

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...

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...

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...

summarize_numerical: Summarize numerical data over groupings of annotated regions

tidy_annotations: Function to tidy up annotation accessors for visualization

Functions

annotate_regions Man page
annotations Man page
annotatr Man page
annotatr_cache Man page
annotatr-package Man page
build_ah_annots Man page
build_annotations Man page
build_cpg_annots Man page
build_enhancer_annots Man page
build_gene_annots Man page
build_hmm_annots Man page
build_lncrna_annots Man page
builtin_annotations Man page
builtin_genomes Man page
check_annotations Man page
expand_annotations Man page
get_cellline_from_code Man page
get_cellline_from_shortcut Man page
get_orgdb_name Man page
get_txdb_name Man page
plot_annotation Man page
plot_categorical Man page
plot_coannotations Man page
plot_numerical Man page
plot_numerical_coannotations Man page
randomize_regions Man page
read_annotations Man page
read_regions Man page
reformat_hmm_codes Man page
subset_order_tbl Man page
summarize_annotations Man page
summarize_categorical Man page
summarize_numerical Man page
tidy_annotations Man page

Files

DESCRIPTION
NAMESPACE
R
R/annotatr_data_doc.R R/annotatr_package_doc.R R/build_annotations.R R/intersect.R R/randomize.R R/read.R R/summarize.R R/utils.R R/visualize.R
build
build/vignette.rds
data
data/annotations.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/annotatr-vignette.R
inst/doc/annotatr-vignette.Rmd
inst/doc/annotatr-vignette.html
inst/extdata
inst/extdata/Gm12878_Ezh2_peak_annotations.txt.gz
inst/extdata/Gm12878_Ezh2_sorted_scores.narrowPeak.gz
inst/extdata/Gm12878_Stat3_chr2.bed.gz
inst/extdata/IDH2mut_v_NBM_multi_data_chr9.txt.gz
inst/extdata/K562_Cjun_peak_annotations.txt.gz
inst/extdata/test_BED3.bed
inst/extdata/test_BED4.bed
inst/extdata/test_BED5.bed
inst/extdata/test_BED6.bed
inst/extdata/test_annotation_nooverlap.bed
inst/extdata/test_annotations_3.bed
inst/extdata/test_annotations_4.bed
inst/extdata/test_annotations_5.bed
inst/extdata/test_annotations_6.bed
inst/extdata/test_annotations_6_gene.bed
inst/extdata/test_annotations_6_symbol.bed
inst/extdata/test_annotations_6_tx_gene_symbol.bed
inst/extdata/test_annotations_minoverlap.bed
inst/extdata/test_bedGraph.bedGraph
inst/extdata/test_intersect.bed
inst/extdata/test_read_multiple_data_nohead.bed
man
man/annotate_regions.Rd man/annotations.Rd man/annotatr.Rd man/annotatr_cache.Rd man/build_ah_annots.Rd man/build_annotations.Rd man/build_cpg_annots.Rd man/build_enhancer_annots.Rd man/build_gene_annots.Rd man/build_hmm_annots.Rd man/build_lncrna_annots.Rd man/builtin_annotations.Rd man/builtin_genomes.Rd man/check_annotations.Rd man/expand_annotations.Rd man/get_cellline_from_code.Rd man/get_cellline_from_shortcut.Rd man/get_orgdb_name.Rd man/get_txdb_name.Rd man/plot_annotation.Rd man/plot_categorical.Rd man/plot_coannotations.Rd man/plot_numerical.Rd man/plot_numerical_coannotations.Rd man/randomize_regions.Rd man/read_annotations.Rd man/read_regions.Rd man/reformat_hmm_codes.Rd man/subset_order_tbl.Rd man/summarize_annotations.Rd man/summarize_categorical.Rd man/summarize_numerical.Rd man/tidy_annotations.Rd
tests
tests/testthat
tests/testthat.R tests/testthat/test_1_utils.R tests/testthat/test_2_read.R tests/testthat/test_3_build_annotations.R tests/testthat/test_4_intersect.R tests/testthat/test_5_randomize.R tests/testthat/test_6_summarize.R tests/testthat/test_7_visualize.R
vignettes
vignettes/annotatr-vignette.Rmd
vignettes/annotatr_cpgs.jpeg
vignettes/annotatr_genes.jpeg

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