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

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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.

Author
P. Aboyoun, H. Pag├Ęs, and M. Lawrence
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0
Version
1.26.1

View on Bioconductor

Man pages

absoluteRanges
Transform genomic ranges into "absolute" ranges
constraint
Enforcing constraints thru Constraint objects
coverage-methods
Coverage of a GRanges or GRangesList object
DelegatingGenomicRanges-class
DelegatingGenomicRanges objects
findOverlaps-methods
Finding overlapping genomic ranges
GenomicRanges-comparison
Comparing and ordering genomic ranges
GenomicRangesList-class
GenomicRangesList objects
genomicvars
Manipulating genomic variables
GNCList-class
GNCList objects
GPos-class
GPos objects
GRanges-class
GRanges objects
GRangesList-class
GRangesList objects
inter-range-methods
Inter range transformations of a GRanges or GRangesList...
intra-range-methods
Intra range transformations of a GRanges or GRangesList...
makeGRangesFromDataFrame
Make a GRanges object from a data.frame or DataFrame
makeGRangesListFromDataFrame
Make a GRangesList object from a data.frame or DataFrame
nearest-methods
Finding the nearest genomic range neighbor
phicoef
Calculate the "phi coefficient" between two binary variables
range-squeezers
Squeeze the ranges out of a range-based object
setops-methods
Set operations on genomic ranges
strand-utils
Strand utilities
tileGenome
Put (virtual) tiles on a given genome
tile-methods
Generate windows for a GenomicRanges

Files in this package

GenomicRanges/DESCRIPTION
GenomicRanges/NAMESPACE
GenomicRanges/NEWS
GenomicRanges/R
GenomicRanges/R/DelegatingGenomicRanges-class.R
GenomicRanges/R/GNCList-class.R
GenomicRanges/R/GPos-class.R
GenomicRanges/R/GRanges-class.R
GenomicRanges/R/GRangesList-class.R
GenomicRanges/R/GenomicRanges-class.R
GenomicRanges/R/GenomicRanges-comparison.R
GenomicRanges/R/GenomicRangesList-class.R
GenomicRanges/R/RangedData-methods.R
GenomicRanges/R/absoluteRanges.R
GenomicRanges/R/constraint.R
GenomicRanges/R/coverage-methods.R
GenomicRanges/R/findOverlaps-methods.R
GenomicRanges/R/genomicvars.R
GenomicRanges/R/inter-range-methods.R
GenomicRanges/R/intra-range-methods.R
GenomicRanges/R/makeGRangesFromDataFrame.R
GenomicRanges/R/makeGRangesListFromDataFrame.R
GenomicRanges/R/nearest-methods.R
GenomicRanges/R/phicoef.R
GenomicRanges/R/range-squeezers.R
GenomicRanges/R/setops-methods.R
GenomicRanges/R/strand-utils.R
GenomicRanges/R/tile-methods.R
GenomicRanges/R/tileGenome.R
GenomicRanges/R/transcript-utils.R
GenomicRanges/R/utils.R
GenomicRanges/R/zzz.R
GenomicRanges/build
GenomicRanges/build/vignette.rds
GenomicRanges/inst
GenomicRanges/inst/CITATION
GenomicRanges/inst/doc
GenomicRanges/inst/doc/ExtendingGenomicRanges.R
GenomicRanges/inst/doc/ExtendingGenomicRanges.Rnw
GenomicRanges/inst/doc/ExtendingGenomicRanges.pdf
GenomicRanges/inst/doc/GRanges_and_GRangesList_slides.R
GenomicRanges/inst/doc/GRanges_and_GRangesList_slides.Rnw
GenomicRanges/inst/doc/GRanges_and_GRangesList_slides.pdf
GenomicRanges/inst/doc/GenomicRangesHOWTOs.R
GenomicRanges/inst/doc/GenomicRangesHOWTOs.Rnw
GenomicRanges/inst/doc/GenomicRangesHOWTOs.pdf
GenomicRanges/inst/doc/GenomicRangesIntroduction.R
GenomicRanges/inst/doc/GenomicRangesIntroduction.Rnw
GenomicRanges/inst/doc/GenomicRangesIntroduction.pdf
GenomicRanges/inst/doc/Ten_things_slides.R
GenomicRanges/inst/doc/Ten_things_slides.Rnw
GenomicRanges/inst/doc/Ten_things_slides.pdf
GenomicRanges/inst/extdata
GenomicRanges/inst/extdata/feature_frags.txt
GenomicRanges/inst/scripts
GenomicRanges/inst/scripts/timing_overlaps.R
GenomicRanges/inst/unitTests
GenomicRanges/inst/unitTests/test_GNCList-class.R
GenomicRanges/inst/unitTests/test_GRanges-class.R
GenomicRanges/inst/unitTests/test_GRangesList-class.R
GenomicRanges/inst/unitTests/test_GenomicRanges-comparison.R
GenomicRanges/inst/unitTests/test_coverage-methods.R
GenomicRanges/inst/unitTests/test_findOverlaps-methods.R
GenomicRanges/inst/unitTests/test_inter-range-methods.R
GenomicRanges/inst/unitTests/test_intra-range-methods.R
GenomicRanges/inst/unitTests/test_makeGRangesFromDataFrame.R
GenomicRanges/inst/unitTests/test_makeGRangesListFromDataFrame.R
GenomicRanges/inst/unitTests/test_nearest-methods.R
GenomicRanges/inst/unitTests/test_setops-methods.R
GenomicRanges/man
GenomicRanges/man/DelegatingGenomicRanges-class.Rd
GenomicRanges/man/GNCList-class.Rd
GenomicRanges/man/GPos-class.Rd
GenomicRanges/man/GRanges-class.Rd
GenomicRanges/man/GRangesList-class.Rd
GenomicRanges/man/GenomicRanges-comparison.Rd
GenomicRanges/man/GenomicRangesList-class.Rd
GenomicRanges/man/absoluteRanges.Rd
GenomicRanges/man/constraint.Rd
GenomicRanges/man/coverage-methods.Rd
GenomicRanges/man/findOverlaps-methods.Rd
GenomicRanges/man/genomicvars.Rd
GenomicRanges/man/inter-range-methods.Rd
GenomicRanges/man/intra-range-methods.Rd
GenomicRanges/man/makeGRangesFromDataFrame.Rd
GenomicRanges/man/makeGRangesListFromDataFrame.Rd
GenomicRanges/man/nearest-methods.Rd
GenomicRanges/man/phicoef.Rd
GenomicRanges/man/range-squeezers.Rd
GenomicRanges/man/setops-methods.Rd
GenomicRanges/man/strand-utils.Rd
GenomicRanges/man/tile-methods.Rd
GenomicRanges/man/tileGenome.Rd
GenomicRanges/src
GenomicRanges/src/GenomicRanges.h
GenomicRanges/src/IRanges_stubs.c
GenomicRanges/src/R_init_GenomicRanges.c
GenomicRanges/src/S4Vectors_stubs.c
GenomicRanges/src/transcript_utils.c
GenomicRanges/tests
GenomicRanges/tests/run_unitTests.R
GenomicRanges/vignettes
GenomicRanges/vignettes/ExtendingGenomicRanges.Rnw
GenomicRanges/vignettes/GRanges_and_GRangesList_slides.Rnw
GenomicRanges/vignettes/GenomicRanges.bib
GenomicRanges/vignettes/GenomicRangesHOWTOs.Rnw
GenomicRanges/vignettes/GenomicRangesIntroduction.Rnw
GenomicRanges/vignettes/Ten_things_slides.Rnw
GenomicRanges/vignettes/slides.sty