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.

AuthorRaymond G. Cavalcante [aut, cre], Maureen A. Sartor [ths]
Date of publicationNone
MaintainerRaymond G. Cavalcante <rcavalca@umich.edu>
LicenseGPL-3
Version1.0.3

View on Bioconductor

Man pages

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

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

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

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_lncrna_annots: A helper function to build lncRNA annotations.

check_annotations: Function to check for valid annotations

expand_annotations: Function to expand annotation shortcuts

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

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

supported_annotations: Function listing which annotations are available.

supported_genomes: Function returning supported TxDb.* genomes

tidy_annotations: Function to tidy up annotation accessors for visualization

Functions

annotate_regions Man page
annotatr Man page
annotatr_cache Man page
annotatr-package Man page
build_annotations Man page
build_cpg_annots Man page
build_enhancer_annots Man page
build_gene_annots Man page
build_lncrna_annots Man page
check_annotations Man page
expand_annotations 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
subset_order_tbl Man page
summarize_annotations Man page
summarize_categorical Man page
summarize_numerical Man page
supported_annotations Man page
supported_genomes Man page
tidy_annotations Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.