Package: GenomicRanges 1.59.1
Hervé Pagès
GenomicRanges: Representation and manipulation of genomic intervals
The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.
Authors:
GenomicRanges_1.59.1.tar.gz
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GenomicRanges.pdf |GenomicRanges.html✨
GenomicRanges/json (API)
NEWS
| # Install 'GenomicRanges' in R: |
| install.packages('GenomicRanges', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/genomicranges/issues
On BioConductor:GenomicRanges-1.59.1(bioc 3.21)GenomicRanges-1.58.0(bioc 3.20)
geneticsinfrastructuredatarepresentationsequencingannotationgenomeannotationcoveragebioconductor-packagecore-package
Last updated 1 months agofrom:efa80fa13a. Checks:OK: 6 ERROR: 2 NOTE: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win-x86_64 | NOTE | Dec 19 2024 |
| R-4.5-linux-x86_64 | ERROR | Dec 19 2024 |
| R-4.4-win-x86_64 | OK | Dec 19 2024 |
| R-4.4-mac-x86_64 | OK | Dec 19 2024 |
| R-4.4-mac-aarch64 | OK | Dec 19 2024 |
| R-4.3-win-x86_64 | ERROR | Dec 19 2024 |
| R-4.3-mac-x86_64 | OK | Dec 19 2024 |
| R-4.3-mac-aarch64 | OK | Dec 19 2024 |
Exports:.DollarNames.GenomicRanges.DollarNames.GRangesabsoluteRangesas.data.frameas.data.frame.GPosas.factorbindAsGRangesbindROWSbinnedAveragecheckConstraintcoercecountOverlapscoveragedisjoindisjointBinsdistancedistanceToNearestduplicatedduplicated.GenomicRangeselementMetadataelementMetadata<-endend<-FactorToClassfindOverlapsflankfollowfrom_GPos_to_GRangesgapsGNCListGPosgrangesGRangesGRangesFactorGRangesListgrglistintersectinvertStrandis.unsortedisDisjointisSmallGenomemakeGRangesFromDataFramemakeGRangesListFromDataFramemakeGRangesListFromFeatureFragmentsmatchmcolAsRleListmcolsmcols<-mergenarrownearestnearestKNeighborsOpsorderparallel_slot_namespcomparepgapphicoefpintersectposprecedepromoterspsetdiffpunionrangesranges<-rankreducerelativeRangesrelistToClassresizerestrictrglistscorescore<-selfmatchseqinfoseqinfo<-seqnamesseqnames<-setdiffshiftshowslidingWindowssortsort.GenomicRangessort.GRangesListsplitstartstart<-strandstrand<-subtractsummarysummary.GenomicRangessummary.GPosterminatorstiletileGenometrimunionupdateupdate_rangesupdateObjectvaluesvalues<-widthwidth<-windows
Dependencies:askpassBiocGenericscurlgenericsGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitemimeopensslR6S4VectorssysUCSC.utilsXVectorzlibbioc
An Introduction to the GenomicRanges Package
Rendered fromGenomicRangesIntroduction.Rmdusingknitr::rmarkdownon Dec 19 2024.Last update: 2024-06-10
Started: 2018-07-30
GenomicRanges HOWTOs
Rendered fromGenomicRangesHOWTOs.Rnwusingutils::Sweaveon Dec 19 2024.Last update: 2024-06-10
Started: 2013-10-25
A quick introduction to GRanges and GRangesList objects (slides)
Rendered fromGRanges_and_GRangesList_slides.Rnwusingutils::Sweaveon Dec 19 2024.Last update: 2020-10-07
Started: 2015-02-04
Ten Things You Didn't Know (slides from BioC 2016)
Rendered fromTen_things_slides.Rnwusingutils::Sweaveon Dec 19 2024.Last update: 2022-12-07
Started: 2016-06-25
Extending GenomicRanges
Rendered fromExtendingGenomicRanges.Rnwusingutils::Sweaveon Dec 19 2024.Last update: 2016-12-13
Started: 2014-10-03
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Transform genomic ranges into "absolute" ranges | absoluteRanges isSmallGenome relativeRanges |
| Enforcing constraints thru Constraint objects | checkConstraint class:Constraint class:Constraint_OR_NULL Constraint constraint Constraint-class constraint<- Constraints Constraint_OR_NULL Constraint_OR_NULL-class |
| Coverage of a GRanges or GRangesList object | coverage coverage,GenomicRanges-method coverage,GRangesList-method coverage,StitchedGPos-method coverage-methods |
| DelegatingGenomicRanges objects | class:DelegatingGenomicRanges DelegatingGenomicRanges-class ranges,DelegatingGenomicRanges-method seqinfo,DelegatingGenomicRanges-method seqnames,DelegatingGenomicRanges-method strand,DelegatingGenomicRanges-method update,DelegatingGenomicRanges-method |
| Finding overlapping genomic ranges | countOverlaps countOverlaps,GenomicRanges,GenomicRanges-method findOverlaps findOverlaps,GenomicRanges,GenomicRanges-method findOverlaps,GenomicRanges,GRangesList-method findOverlaps,GRangesList,GenomicRanges-method findOverlaps,GRangesList,GRangesList-method findOverlaps-methods overlapsAny subsetByOverlaps |
| Squeeze the genomic ranges out of a range-based object | genomic-range-squeezers granges grglist grglist,Pairs-method |
| Comparing and ordering genomic ranges | duplicated,GenomicRanges-method duplicated.GenomicRanges GenomicRanges-comparison is.unsorted,GenomicRanges-method match,GenomicRanges,GenomicRanges-method order,GenomicRanges-method pcompare pcompare,GenomicRanges,GenomicRanges-method rank,GenomicRanges-method selfmatch,GenomicRanges-method sort,GenomicRanges-method sort.GenomicRanges |
| GenomicRangesList objects | class:CompressedGenomicRangesList class:GenomicRangesList class:GenomicRanges_OR_GenomicRangesList class:SimpleGenomicRangesList CompressedGenomicRangesList CompressedGenomicRangesList-class elementMetadata,GenomicRangesList-method elementMetadata<-,CompressedGenomicRangesList-method end<-,CompressedGenomicRangesList-method extractROWS,GenomicRangesList,ANY-method GenomicRangesList GenomicRangesList-class GenomicRanges_OR_GenomicRangesList GenomicRanges_OR_GenomicRangesList-class getListElement,GenomicRangesList-method length,GenomicRangesList-method names,GenomicRangesList-method names<-,GenomicRangesList-method score,GenomicRangesList-method score<-,GenomicRangesList-method seqinfo,CompressedGenomicRangesList-method seqinfo,GenomicRangesList-method seqinfo<-,CompressedGenomicRangesList-method seqnames,GenomicRangesList-method seqnames<-,CompressedGenomicRangesList-method show,GenomicRangesList-method SimpleGenomicRangesList SimpleGenomicRangesList-class start<-,CompressedGenomicRangesList-method strand,GenomicRangesList-method strand<-,CompressedGenomicRangesList,ANY-method strand<-,CompressedGenomicRangesList,character-method unlist,GenomicRangesList-method updateObject,GenomicRangesList-method width<-,CompressedGenomicRangesList-method |
| Manipulating genomic variables | bindAsGRanges binnedAverage coerce,RleList,GRanges-method coerce,RleViewsList,GRanges-method genomicvariables genomicvars mcolAsRleList |
| GNCList objects | class:GNCList coerce,GenomicRanges,GNCList-method coerce,GNCList,GRanges-method end,GNCList-method GNCList GNCList-class granges,GNCList-method length,GNCList-method names,GNCList-method ranges,GNCList-method seqinfo,GNCList-method seqnames,GNCList-method start,GNCList-method strand,GNCList-method width,GNCList-method |
| Memory-efficient representation of genomic positions | as.data.frame,GPos-method as.data.frame.GPos class:GPos class:StitchedGPos class:UnstitchedGPos coerce,ANY,GPos-method coerce,ANY,StitchedGPos-method coerce,ANY,UnstitchedGPos-method coerce,GRanges,GPos-method coerce,GRanges,StitchedGPos-method coerce,GRanges,UnstitchedGPos-method coerce,StitchedGPos,GRanges-method coerce,UnstitchedGPos,GRanges-method from_GPos_to_GRanges GPos GPos-class pos,GPos-method show,GPos-method StitchedGPos StitchedGPos-class summary,GPos-method summary.GPos UnstitchedGPos UnstitchedGPos-class updateObject,GPos-method |
| GRanges objects | $,GenomicRanges-method $<-,GenomicRanges-method as.character,GenomicRanges-method as.data.frame,GenomicRanges-method as.factor,GenomicRanges-method bindROWS,GenomicRanges-method class:GenomicPos class:GenomicRanges class:GRanges class:IRanges_OR_IPos coerce,ANY,GenomicRanges-method coerce,character,GRanges-method coerce,factor,GRanges-method coerce,GenomicRanges,CompressedIRangesList-method coerce,GenomicRanges,GRanges-method coerce,GenomicRanges,Grouping-method coerce,GenomicRanges,IntegerRangesList-method coerce,GenomicRanges,IRangesList-method coerce,IntegerRangesList,GRanges-method coerce,Seqinfo,GRanges-method coerce,Seqinfo,IntegerRangesList-method end<-,GenomicRanges-method GenomicPos GenomicPos-class GenomicRanges GenomicRanges-class GenomicRanges_OR_missing-class getListElement,GenomicRanges-method GRanges granges,GenomicRanges-method GRanges-class IRanges_OR_IPos IRanges_OR_IPos-class length,GenomicRanges-method names,GenomicRanges-method names<-,GenomicRanges-method parallel_slot_names,GRanges-method ranges,GRanges-method ranges<-,GenomicRanges-method score,GenomicRanges-method score<-,GenomicRanges-method seqinfo,GRanges-method seqinfo,List-method seqinfo<-,GenomicRanges-method seqinfo<-,List-method seqnames,GRanges-method seqnames<-,GenomicRanges-method show,GenomicRanges-method start,GenomicRanges-method start<-,GenomicRanges-method strand,GRanges-method strand<-,GenomicRanges,ANY-method summary,GenomicRanges-method summary.GenomicRanges update,GRanges-method updateObject,GRanges-method width,GenomicRanges-method width<-,GenomicRanges-method [,list_OR_List,GenomicRanges-method |
| GRangesFactor objects | class:GRangesFactor coerce,ANY,GRangesFactor-method coerce,Factor,GRanges-method end,GRangesFactor-method FactorToClass,GRanges-method granges,GRangesFactor-method GRangesFactor GRangesFactor-class pos,GRangesFactor-method ranges,GRangesFactor-method seqinfo,GRangesFactor-method seqnames,GRangesFactor-method show,GRangesFactor-method start,GRangesFactor-method strand,GRangesFactor-method width,GRangesFactor-method |
| GRangesList objects | class:CompressedGRangesList class:GenomicRanges_OR_GRangesList class:GRangesList class:SimpleGRangesList coerce,CompressedGRangesList,CompressedIRangesList-method coerce,CompressedGRangesList,IntegerRangesList-method coerce,CompressedGRangesList,IRangesList-method coerce,GenomicRangesList,SimpleGRangesList-method coerce,List,CompressedGRangesList-method coerce,list,CompressedGRangesList-method coerce,List,GRangesList-method coerce,list,GRangesList-method coerce,List,SimpleGRangesList-method coerce,list,SimpleGRangesList-method coerce,SimpleGenomicRangesList,SimpleGRangesList-method coerce,SimpleList,SimpleGRangesList-method CompressedGRangesList CompressedGRangesList-class GenomicRanges_OR_GRangesList GenomicRanges_OR_GRangesList-class GRangesList GRangesList-class makeGRangesListFromFeatureFragments ranges,CompressedGRangesList-method ranges<-,CompressedGRangesList-method relistToClass,GRanges-method SimpleGRangesList SimpleGRangesList-class sort,CompressedGRangesList-method sort,GRangesList-method sort.GRangesList [,CompressedGRangesList,ANY-method [<-,CompressedGRangesList,ANY,ANY,ANY-method [<-,CompressedGRangesList,ANY-method [<-,CompressedGRangesList-method |
| Inter range transformations of a GRanges or GRangesList object | disjoin disjoin,GenomicRanges-method disjoin,GRangesList-method disjointBins disjointBins,GenomicRanges-method gaps gaps,GenomicRanges-method inter-range-methods isDisjoint isDisjoint,GenomicRanges-method isDisjoint,GRangesList-method isDisjoint,StitchedGPos-method range range,GenomicRanges-method range,GRangesList-method range,StitchedGPos-method reduce reduce,GenomicRanges-method reduce,GRangesList-method |
| Intra range transformations of a GRanges or GRangesList object | flank flank,GenomicRanges-method intra-range-methods narrow narrow,GenomicRanges-method promoters promoters,GenomicRanges-method resize resize,GenomicRanges-method restrict restrict,GenomicRanges-method shift shift,GenomicRanges-method terminators terminators,GenomicRanges-method trim trim,GenomicRanges-method trim,GRangesList-method update_ranges,GenomicRanges-method |
| Make a GRanges object from a data.frame or DataFrame | coerce,data.frame,GRanges-method coerce,DataFrame,GRanges-method makeGRangesFromDataFrame |
| Make a GRangesList object from a data.frame or DataFrame | makeGRangesListFromDataFrame |
| Finding the nearest genomic range/position neighbor | distance distance,GenomicRanges,GenomicRanges-method distanceToNearest distanceToNearest,GenomicRanges,GenomicRanges-method distanceToNearest,GenomicRanges,missing-method follow follow,GenomicRanges,GenomicRanges-method follow,GenomicRanges,missing-method nearest nearest,GenomicRanges,GenomicRanges-method nearest,GenomicRanges,missing-method nearest-methods nearestKNeighbors nearestKNeighbors,GenomicRanges,GenomicRanges-method nearestKNeighbors,GenomicRanges,missing-method precede precede,GenomicRanges,GenomicRanges-method precede,GenomicRanges,missing-method |
| Calculate the "phi coefficient" between two binary variables | phicoef |
| Set operations on genomic ranges | intersect intersect,GenomicRanges,GenomicRanges-method intersect,GenomicRanges,Vector-method intersect,GRangesList,GRangesList-method intersect,Vector,GenomicRanges-method pgap pgap,GRanges,GRanges-method pintersect pintersect,GRanges,GRanges-method pintersect,GRanges,GRangesList-method pintersect,GRangesList,GRanges-method psetdiff psetdiff,GRanges,GRanges-method psetdiff,GRanges,GRangesList-method punion punion,GRanges,GRanges-method punion,GRanges,GRangesList-method punion,GRangesList,GRanges-method setdiff setdiff,GenomicRanges,GenomicRanges-method setdiff,GenomicRanges,Vector-method setdiff,GRangesList,GRangesList-method setdiff,Vector,GenomicRanges-method setops-methods union union,GenomicRanges,GenomicRanges-method union,GenomicRanges,Vector-method union,GRangesList,GRangesList-method union,Vector,GenomicRanges-method |
| Strand utilities | invertStrand,character-method invertStrand,factor-method invertStrand,integer-method invertStrand,logical-method invertStrand,NULL-method invertStrand,Rle-method invertStrand,RleList-method strand,character-method strand,DataFrame-method strand,factor-method strand,integer-method strand,logical-method strand,missing-method strand,NULL-method strand,Rle-method strand,RleList-method strand-utils strand<-,DataFrame,ANY-method |
| Subtract a set of genomic ranges from a GRanges object | subtract subtract,GenomicRanges,GenomicRanges-method subtract-methods |
| Generate windows for a GenomicRanges | slidingWindows slidingWindows,GenomicRanges-method tile tile,GenomicRanges-method tile-methods |
| Put (virtual) tiles on a given genome | tileGenome |
