GenomicRanges v1.24.1

Representation and manipulation of genomic intervals and variables defined along a genome

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.

Functions in GenomicRanges

Name	Description
intra-range-methods	Intra range transformations of a GRanges or GRangesList object
GenomicRanges-comparison	Comparing and ordering genomic ranges
phicoef	Calculate the "phi coefficient" between two binary variables
DelegatingGenomicRanges-class	DelegatingGenomicRanges objects
tileGenome	Put (virtual) tiles on a given genome
setops-methods	Set operations on genomic ranges
Constraints	Enforcing constraints thru Constraint objects
absoluteRanges	Transform genomic ranges into "absolute" ranges
nearest-methods	Finding the nearest genomic range neighbor
coverage-methods	Coverage of a GRanges or GRangesList object
GenomicRangesList-class	GenomicRangesList objects
GRangesList-class	GRangesList objects
makeGRangesFromDataFrame	Make a GRanges object from a data.frame or DataFrame
tile-methods	Tile a GenomicRanges object
GRanges-class	GRanges objects
GPos-class	GPos objects
GNCList-class	GNCList objects
inter-range-methods	Inter range transformations of a GRanges or GRangesList object
findOverlaps-methods	Finding overlapping genomic ranges
range-squeezers	Squeeze the ranges out of a range-based object
genomicvars	Manipulating genomic variables
strand-utils	Strand utilities
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Encoding	UTF-8
biocViews	Genetics, Infrastructure, Sequencing, Annotation, Coverage, GenomeAnnotation
LinkingTo	S4Vectors, IRanges
License	Artistic-2.0
Collate	utils.R phicoef.R transcript-utils.R constraint.R strand-utils.R range-squeezers.R GenomicRanges-class.R GenomicRanges-comparison.R GRanges-class.R GPos-class.R DelegatingGenomicRanges-class.R GNCList-class.R GenomicRangesList-class.R GRangesList-class.R makeGRangesFromDataFrame.R RangedData-methods.R findOverlaps-methods.R intra-range-methods.R inter-range-methods.R coverage-methods.R setops-methods.R nearest-methods.R absoluteRanges.R tileGenome.R tile-methods.R genomicvars.R zzz.R

suggests	annotate , AnnotationDbi (>= 1.21.1) , AnnotationHub , Biobase , BiocStyle , Biostrings (>= 2.25.3) , BSgenome , BSgenome.Hsapiens.UCSC.hg19 , BSgenome.Scerevisiae.UCSC.sacCer2 , DESeq2 , DEXSeq , digest , edgeR , GenomicAlignments , GenomicFeatures , Gviz , hgu95av2 , hgu95av2.db , KEGG , KEGG.db , KEGGgraph , Matrix , org , org.Hs.eg.db , org.Mm.eg.db , org.Sc.sgd.db , pasilla , pasillaBamSubset , Rsamtools (>= 1.13.53) , rtracklayer , RUnit , SummarizedExperiment (>= 0.1.5) , TxDb , TxDb.Athaliana.BioMart.plantsmart22 , TxDb.Dmelanogaster.UCSC.dm3.ensGene , TxDb.Hsapiens.UCSC.hg19.knownGene , VariantAnnotation
depends	base (>= 2.10) , BiocGenerics (>= 0.17.5) , GenomeInfoDb (>= 1.1.20) , IRanges (>= 2.5.36) , methods , R (>= 2.10) , S4Vectors (>= 0.9.47)
imports	stats , utils , XVector
Contributors	H. Pagès, P. Aboyoun, M. Lawrence

GenomicRanges v1.24.1

Representation and manipulation of genomic intervals and variables defined along a genome

Functions in GenomicRanges

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