Package: annotatr 1.33.0
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:
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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')) |
Bug tracker:https://github.com/rcavalcante/annotatr/issues
- annotations - Example_annotations data
On BioConductor:annotatr-1.33.0(bioc 3.21)annotatr-1.32.0(bioc 3.20)
softwareannotationgenomeannotationfunctionalgenomicsvisualizationgenome-annotation
Last updated 3 months agofrom:d81bd7bb38. Checks:1 OK, 6 NOTE. Indexed: yes.
Target | Result | Latest binary |
---|---|---|
Doc / Vignettes | OK | Jan 20 2025 |
R-4.5-win | NOTE | Jan 20 2025 |
R-4.5-linux | NOTE | Jan 20 2025 |
R-4.4-win | NOTE | Jan 20 2025 |
R-4.4-mac | NOTE | Jan 20 2025 |
R-4.3-win | NOTE | Jan 20 2025 |
R-4.3-mac | NOTE | Jan 20 2025 |
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.utilsutf8vctrsviridisLitevroomwithrXMLXVectoryaml