Package: GenomicRanges 1.57.1

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:Patrick Aboyoun [aut], Hervé Pagès [aut, cre], Michael Lawrence [aut], Sonali Arora [ctb], Martin Morgan [ctb], Kayla Morrell [ctb], Valerie Obenchain [ctb], Marcel Ramos [ctb], Lori Shepherd [ctb], Dan Tenenbaum [ctb], Daniel van Twisk [ctb]

# 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-1.57.0(bioc 3.20)GenomicRanges-1.56.0(bioc 3.19)

bioconductor-package

109 exports 12.81 score 16 dependencies 1258 dependents 323 mentions

Last updated 30 days agofrom:2b7bf7d519

Exports:.DollarNames.GenomicRanges .DollarNames.GRanges absoluteRanges as.data.frame as.data.frame.GPos as.factor bindAsGRanges bindROWS binnedAverage checkConstraint coerce countOverlaps coverage disjoin disjointBins distance distanceToNearest duplicated duplicated.GenomicRanges elementMetadata elementMetadata<-end end<-FactorToClass findOverlaps flank follow from_GPos_to_GRanges gaps GNCList GPos granges GRanges GRangesFactor GRangesList grglist intersect invertStrand is.unsorted isDisjoint isSmallGenome makeGRangesFromDataFrame makeGRangesListFromDataFrame makeGRangesListFromFeatureFragments match mcolAsRleList mcols mcols<-merge narrow nearest nearestKNeighbors Ops order parallel_slot_names pcompare pgap phicoef pintersect pos precede promoters psetdiff punion ranges ranges<-rank reduce relativeRanges relistToClass resize restrict rglist score score<-selfmatch seqinfo seqinfo<-seqnames seqnames<-setdiff shift show slidingWindows sort sort.GenomicRanges sort.GRangesList split start start<-strand strand<-subtract summary summary.GenomicRanges summary.GPos terminators tile tileGenome trim union update update_ranges updateObject values values<-width width<-windows

Dependencies:askpass BiocGenerics curl GenomeInfoDb GenomeInfoDbData httr IRanges jsonlite mime openssl R6 S4Vectors sys UCSC.utils XVector zlibbioc

An Introduction to the GenomicRanges Package

Marc Carlson, Patrick Aboyoun, Hervé Pagès, and Martin Morgan

Rendered fromGenomicRangesIntroduction.Rmdusingknitr::rmarkdownon Jun 11 2024.

Last update: 2024-06-10
Started: 2018-07-30

GenomicRanges HOWTOs

Rendered fromGenomicRangesHOWTOs.Rnwusingutils::Sweaveon Jun 11 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 Jun 11 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 Jun 11 2024.

Last update: 2022-12-07
Started: 2016-06-25

Extending GenomicRanges

Rendered fromExtendingGenomicRanges.Rnwusingutils::Sweaveon Jun 11 2024.

Last update: 2016-12-13
Started: 2014-10-03

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

Package: GenomicRanges 1.57.1

GenomicRanges: Representation and manipulation of genomic intervals

An Introduction to the GenomicRanges Package

GenomicRanges HOWTOs

A quick introduction to GRanges and GRangesList objects (slides)

Ten Things You Didn't Know (slides from BioC 2016)

Extending GenomicRanges

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)