Introduction | Installation | Quick start | Enhanced format support | Comma-separated coordinates | Space-delimited coordinates | Complex chromosome names | Automatic object type detection | Single positions vs. ranges | Genomic interactions | IRanges for non-genomic coordinates | Forcing object types | Working with vectors | Explicit conversion functions | Class detection without parsing | Session Information
Package: GenomicCoordinates 1.1.0
Jacques Serizay
GenomicCoordinates: Enhanced string parsing for genomic coordinates
Extends string parsing capabilities for genomic coordinates, supporting various formats including comma-separated numbers, space-delimited coordinates, and automatic detection of GRanges, GPos, and GInteractions objects.
Authors:
GenomicCoordinates_1.1.0.tar.gz
GenomicCoordinates_1.1.0.zip(r-4.7)GenomicCoordinates_1.1.0.zip(r-4.6)GenomicCoordinates_1.1.0.zip(r-4.5)
GenomicCoordinates_1.1.0.tgz(r-4.6-any)GenomicCoordinates_1.1.0.tgz(r-4.5-any)
GenomicCoordinates_1.1.0.tar.gz(r-4.7-any)GenomicCoordinates_1.1.0.tar.gz(r-4.6-any)
GenomicCoordinates_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
GenomicCoordinates/json (API)
| # Install 'GenomicCoordinates' in R: |
| install.packages('GenomicCoordinates', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/js2264/genomiccoordinates/issues
On BioConductor:GenomicCoordinates-1.1.0(bioc 3.24)GenomicCoordinates-1.0.0(bioc 3.23)
infrastructuredatarepresentationgenomeannotation
Last updated from:0a24b7ecf4. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 208 | ||
| linux-devel-x86_64 | OK | 348 | ||
| source / vignettes | OK | 279 | ||
| linux-release-x86_64 | OK | 402 | ||
| macos-release-arm64 | OK | 199 | ||
| macos-oldrel-arm64 | OK | 168 | ||
| windows-devel | OK | 262 | ||
| windows-release | OK | 285 | ||
| windows-oldrel | OK | 249 | ||
| wasm-release | OK | 197 |
Exports:as_ginteractionsas_gposas_grangesas_irangesdetect_genomic_classGenomicCoordinates
Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopscigarilloclicodetoolscpp11crayoncurlDelayedArraydplyrformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluehttrInteractionSetIRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigplyinteractionsplyrangesR6RcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsystibbletidyselectutf8vctrswithrXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Handle special genomic string formats | .handle_special_formats |
| Additional helper functions for corner cases | .is_single_position |
| Convert to GPos object | as_gpos |
| Conversion methods for genomic coordinates | as_ginteractions,character-method as_gpos,character-method as_granges,character-method as_iranges,character-method coercion |
| Detect the appropriate class for genomic strings | detect_genomic_class |
| GenomicCoordinates: Main parsing function | GenomicCoordinates |
| Re-exported functions from plyranges and plyinteractions | as_ginteractions as_granges as_iranges reexports |
