Package: annotatr 1.39.0

Raymond G. Cavalcante

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.

Authors:Raymond G. Cavalcante [aut, cre], Maureen A. Sartor [ths]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
annotatr/json (API)

# Install 'annotatr' in R:

install.packages('annotatr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rcavalcante/annotatr/issues

Datasets:

annotations - Example_annotations data

On BioConductor:annotatr-1.39.0(bioc 3.24)annotatr-1.38.0(bioc 3.23)

software annotation genomeannotation functionalgenomics visualization genome-annotation

10.27 score 27 stars 5 packages 513 scripts 15 mentions 20 exports 109 dependencies

Last updated from:1cae07bfcd. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	665
linux-devel-x86_64	NOTE	914
source / vignettes	OK	845
linux-release-x86_64	NOTE	929
macos-release-arm64	NOTE	478
macos-oldrel-arm64	NOTE	498
windows-devel	NOTE	601
windows-release	NOTE	696
windows-oldrel	NOTE	620
wasm-release	OK	650

Exports:annotate_regions annotatr_cache build_ah_annots build_annotations builtin_annotations builtin_genomes expand_annotations plot_annotation plot_categorical plot_coannotations plot_numerical plot_numerical_coannotations randomize_regions read_annotations read_regions subset_order_tbl summarize_annotations summarize_categorical summarize_numerical tidy_annotations

Dependencies:abind AnnotationDbi AnnotationHub askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli clipr codetools cpp11 crayon curl DBI dbplyr DelayedArray dplyr farver fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable hms httr httr2 IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plyr png prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp RCurl readr regioneR reshape2 restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML XVector yaml

annotatr: Making sense of genomic regions

Rendered fromannotatr-vignette.Rmdusingknitr::rmarkdown

Last update: 2021-10-21
Started: 2016-10-12

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

Package: annotatr 1.39.0

annotatr: Annotation of Genomic Regions to Genomic Annotations

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