annotatr annotates genomic regions (e.g. differentially methylated regions, ChIP-seq peaks, or SNPs) to genomic features: genes, CpG islands, enhancers, ENCODE cCREs, lncRNAs, chromatin states, and custom annotations. It then summarizes and plots the annotated regions.
annotatr is a Bioconductor package:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("annotatr")
Which annotations are available for which genome builds, from builtin_annotations_table():
| genome | genes | mane | canonical | cpgs | enhancers | chromatin | lncrna | ccres |
|---|---|---|---|---|---|---|---|---|
| dm3 | ✓ | |||||||
| dm6 | ✓ | ✓ | ||||||
| danRer10 | ✓ | ✓ | ||||||
| danRer11 | ✓ | ✓ | ✓ | |||||
| galGal5 | ✓ | ✓ | ||||||
| hg19 | ✓ | ✓ | ✓ | ✓ | ✓ | |||
| hg38 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
| mm9 | ✓ | ✓ | ✓ | |||||
| mm10 | ✓ | ✓ | ✓ | ✓ | ✓ | |||
| mm39 | ✓ | ✓ | ✓ | |||||
| oviariramb2 | ✓ | ✓ | ✓ | |||||
| rn4 | ✓ | ✓ | ||||||
| rn5 | ✓ | ✓ | ||||||
| rn6 | ✓ | ✓ | ||||||
| rn7 | ✓ | ✓ | ✓ |
Custom annotations can be read from BED files with read_annotations(), and gene annotations can be built from any TxDb or EnsDb with build_txdb_annotations().
See the package vignette for a fully worked through use case, and news(package = "annotatr") for the changes in each version.
Cavalcante RG, Sartor MA. annotatr: genomic regions in context. Bioinformatics (2017) 33(15):2381-2383. doi:10.1093/bioinformatics/btx183