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GenomicRanges (version 1.20.8)

Representation and manipulation of genomic intervals

Description

The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing data (a.k.a. NGS data). The package defines general purpose containers for storing genomic intervals. Specialized containers for representing and manipulating short alignments against a reference genome are defined in the GenomicAlignments package.

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Version

Version

1.20.8

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in GenomicRanges (1.20.8)

SummarizedExperiment-class

SummarizedExperiment instances
absoluteRanges

Transform genomic ranges into "absolute" ranges
Constraints

Enforcing constraints thru Constraint objects
GenomicRanges-comparison

Comparing and ordering genomic ranges
strand-utils

Strand utilities
findOverlaps-methods

Finding overlapping genomic ranges
tileGenome

Put (virtual) tiles on a given genome
intra-range-methods

Intra range transformations of a GRanges or GRangesList object
tile-methods

Tile a GenomicRanges object
inter-range-methods

Inter range transformations of a GenomicRanges or GRangesList object
nearest-methods

Finding the nearest genomic range neighbor
phicoef

Calculate the "phi coefficient" between two binary variables
GNCList-class

GNCList objects
GRanges-class

GRanges objects
makeGRangesFromDataFrame

Make a GRanges object from a data.frame or DataFrame
makeSummarizedExperimentFromExpressionSet

Make an SummarizedExperiment object from an ExpressionSet
coverage-methods

Coverage of a GRanges or GRangesList object
DelegatingGenomicRanges-class

DelegatingGenomicRanges objects
mapCoords-methods

Mapping ranges between sequences
mappingFunctions

GenomicRangesList-class

GenomicRangesList objects
GIntervalTree-class

GIntervalTree objects
GRangesList-class

GRangesList objects
GRangesMapping-class

GRangesMapping objects
range-squeezers

Squeeze the ranges out of a range-based object
setops-methods

Set operations on GRanges and GRangesList objects