Package: annotatr 1.31.0

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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annotatr.pdf |annotatr.html✨
annotatr/json (API)
NEWS

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

Peer review:

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

Datasets:

On BioConductor:annotatr-1.31.0(bioc 3.20)annotatr-1.30.0(bioc 3.19)

bioconductor-package

20 exports 1.75 score 113 dependencies 4 dependents 15 mentions

Last updated 2 months agofrom:a675e1f340

Exports:annotate_regionsannotatr_cachebuild_ah_annotsbuild_annotationsbuiltin_annotationsbuiltin_genomesexpand_annotationsplot_annotationplot_categoricalplot_coannotationsplot_numericalplot_numerical_coannotationsrandomize_regionsread_annotationsread_regionssubset_order_tblsummarize_annotationssummarize_categoricalsummarize_numericaltidy_annotations

Dependencies:abindAnnotationDbiAnnotationHubaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBSgenomecachemclicliprcodetoolscolorspacecpp11crayoncurlDBIdbplyrDelayedArraydplyrfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehmshttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRCurlreadrregioneRreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLXVectoryamlzlibbioc

annotatr: Making sense of genomic regions

Raymond G. Cavalcante

Rendered fromannotatr-vignette.Rmdusingknitr::rmarkdownon Jun 30 2024.

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

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
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 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.* genomesbuiltin_genomes
Function to check for valid annotationscheck_annotations
Function to expand annotation shortcutsexpand_annotations
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 get correct org.* package name based on genomeget_orgdb_name
Function to get correct TxDb.* package name based on genomeget_txdb_name
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
Read genomic regions in BEDX+Y formatread_regions
Function to recode classes from chromHMM type columnreformat_hmm_codes
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 numerical data over groupings of annotated regionssummarize_numerical
Function to tidy up annotation accessors for visualizationtidy_annotations