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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Details

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

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