Package: annotatr 1.39.19

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]

annotatr_1.39.19.tar.gz
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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:

On BioConductor:annotatr-1.39.19(bioc 3.24)annotatr-1.38.3(bioc 3.23)

softwareannotationgenomeannotationfunctionalgenomicsvisualizationgenome-annotation

9.57 score 27 stars 6 packages 457 scripts 1.4k downloads 15 mentions 25 exports 102 dependencies

Last updated from:4567918a24. Checks:1 WARNING, 8 ERROR, 1 OK. Indexed: yes.

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bioc-checksWARNING440
linux-develERROR754
source / vignettesERROR645
linux-releaseERROR862
macos-releaseERROR539
macos-oldrelERROR538
windows-develERROR574
windows-releaseERROR544
windows-oldrelERROR544
wasm-releaseOK466

Exports:annotate_regionsannotatr_cachebuild_ah_annotsbuild_annotationsbuild_txdb_annotationsbuiltin_annotationsbuiltin_annotations_tablebuiltin_genomesclear_cached_annotationsexpand_annotationslist_cached_annotationsplot_annotationplot_categoricalplot_coannotationsplot_numericalplot_numerical_coannotationsrandomize_regionsread_annotationsread_regionssubset_order_tblsummarize_annotationssummarize_categoricalsummarize_genessummarize_numericaltidy_annotations

Dependencies:AnnotationDbiAnnotationHubaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicliprcodetoolscpp11crayoncurlDBIdbplyrdigestdplyrfarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehmshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglambda.rlifecyclemagrittrmatrixStatsmemoisemimeopensslpillarpkgconfigplyrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRCurlreadrregioneRreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4VectorsS7scalesSeqinfosnowstringistringrsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
A function to intersect user region data with annotation dataannotate_regions
example_annotations dataannotations
annotatr: Annotation of Genomic Regions to Functional Annotationsannotatr-package annotatr
A global-variable to hold custom annotations loaded in an R sessionannotatr_cache
A helper function to build arbitrary annotatinos from AnnotationHubbuild_ah_annots
A function to build annotations from TxDb.* and AnnotationHub resourcesbuild_annotations
A helper function to build ENCODE cCRE annotations.build_ccre_annots
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 to build a TxDb of the MANE Select transcriptsbuild_mane_txdb
Build gene annotations from any TxDb or EnsDbbuild_txdb_annotations
A helper function to build genic annotations from a TxDb or EnsDbbuild_txdb_gene_annots
Function listing which annotations are available.builtin_annotations
Table of builtin annotations by genomebuiltin_annotations_table
Function returning supported TxDb.* genomesbuiltin_genomes
Cached annotationscached-annotations
Function to check for valid annotationscheck_annotations
Function to check regions and annotations are from the same genomecheck_regions_genome
Clear cached annotations and downloadsclear_cached_annotations
Function to find the pairs of annotation types on each regioncoannotation_pairs
Function to download a file, with retries, into the cachedownload_annotation_file
Function to expand annotation shortcutsexpand_annotations
Function to get the cache resource name of a built annotationget_annotation_rname
Function to get the BiocFileCache for the cacheget_bfc
Function to get the directory of the cacheget_cache_dir
Function to get the resource IDs of cache entriesget_cache_rids
Function to return cell line from chromatin annotation codeget_cellline_from_code
Function to return cell line from chromatin annotation shortcutget_cellline_from_shortcut
Function to map any chromosome alias of a genome to its UCSC-style nameget_chrom_aliases
Function to get the Seqinfo of a GenArk genome with UCSC-style namesget_genark_seqinfo
Function to get the URL of a file in the UCSC GenArk hub for a genomeget_genark_url
Function to map gene IDs to gene symbols, Entrez IDs, and Ensembl IDsget_gene_table
Function to get the MANE Select summaryget_mane_summary
Function to get correct org.* package name based on genomeget_orgdb_name
Function to get correct TxDb.* package name based on genomeget_txdb_name
List cached annotations and downloadslist_cached_annotations
Function to load a built annotation from the cacheload_cached_annotation
Plot the number of regions per annotationplot_annotation
Plot a categorical data variable over anotherplot_categorical
Plot pair-wise annotations across regionsplot_coannotations
Plot numerical data over regions or regions summarized over annotationsplot_numerical
Plot numerical data occurring in pairs of annotationsplot_numerical_coannotations
Randomize Regionsrandomize_regions
Read custom annotationsread_annotations
Function to read an ENCODE cCRE registry BED fileread_ccre_bed
Read genomic regions in BEDX+Y formatread_regions
Function to recode classes from chromHMM type columnreformat_hmm_codes
Function to save a built annotation in the cachesave_cached_annotation
Function to give a GRanges the seqinfo of a genomeset_genome_seqinfo
Function to give an annotation the standard mcolsstandardize_mcols
Function to remove the version from Ensembl IDsstrip_id_version
Function to subset a tbl_df or grouped_df by a columnsubset_order_tbl
Summarize annotation countssummarize_annotations
Summarize categorical data over groupings of annotated regionssummarize_categorical
Summarize annotated regions by genesummarize_genes
Summarize numerical data over groupings of annotated regionssummarize_numerical
Function to tidy up annotation accessors for visualizationtidy_annotations
Function to rename sequences to UCSC-style namesucsc_seqlevels