GenomicRanges: 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.

AuthorP. Aboyoun, H. Pag├Ęs, and M. Lawrence
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.26.2

View on Bioconductor

Functions

absoluteRanges Man page
as.character,GenomicRanges-method Man page
as.data.frame,GenomicRanges-method Man page
as.data.frame,GPos-method Man page
as.factor,GenomicRanges-method Man page
bindAsGRanges Man page
binnedAverage Man page
c,GenomicRanges-method Man page
c,GPos-method Man page
checkConstraint Man page
class:Constraint Man page
class:ConstraintORNULL Man page
class:DelegatingGenomicRanges Man page
class:DelegatingGenomicRanges Man page
class:GenomicRanges Man page
class:GenomicRangesList Man page
class:GNCList Man page
class:GPos Man page
class:GRanges Man page
class:GRangesList Man page
class:SimpleGenomicRangesList Man page
coerce,ANY,GenomicRanges-method Man page
coerce,character,GRanges-method Man page
coerce,data.frame,GRanges-method Man page
coerce,DataFrame,GRanges-method Man page
coerce,factor,GRanges-method Man page
coerce,GenomicRanges,GNCList-method Man page
coerce,GenomicRanges,GPos-method Man page
coerce,GenomicRanges,GRanges-method Man page
coerce,GenomicRanges,Grouping-method Man page
coerce,GenomicRangesList,RangedDataList-method Man page
coerce,GenomicRanges,RangedData-method Man page
coerce,GenomicRanges,RangesList-method Man page
coerce,GNCList,GRanges-method Man page
coerce,GRanges,GRangesList-method Man page
coerce,GRangesList,CompressedIRangesList-method Man page
coerce,GRangesList,IRangesList-method Man page
coerce,GRangesList,RangesList-method Man page
coerce,RangedData,GRanges-method Man page
coerce,RangedDataList,GenomicRangesList-method Man page
coerce,RangedDataList,GRangesList-method Man page
coerce,RangesList,GRanges-method Man page
coerce,RleList,GRanges-method Man page
coerce,RleViewsList,GRanges-method Man page
coerce,Seqinfo,GRanges-method Man page
coerce,Seqinfo,RangesList-method Man page
constraint Man page
constraint<- Man page
Constraint Man page
Constraint-class Man page
ConstraintORNULL Man page
ConstraintORNULL-class Man page
Constraints Man page
countOverlaps Man page
countOverlaps,GenomicRanges,GenomicRanges-method Man page
coverage Man page
coverage,GenomicRanges-method Man page
coverage,GRangesList-method Man page
coverage-methods Man page
DelegatingGenomicRanges-class Man page
DelegatingGenomicRanges-class Man page
disjoin Man page
disjoin,GenomicRanges-method Man page
disjoin,GRangesList-method Man page
disjointBins Man page
disjointBins,GenomicRanges-method Man page
distance Man page
distance,GenomicRanges,GenomicRanges-method Man page
distanceToNearest Man page
distanceToNearest,GenomicRanges,GenomicRanges-method Man page
distanceToNearest,GenomicRanges,missing-method Man page
duplicated.GenomicRanges Man page
duplicated,GenomicRanges-method Man page
elementMetadata<-,GRangesList-method Man page
elementMetadata,GRangesList-method Man page
end<-,GenomicRanges-method Man page
end,GenomicRanges-method Man page
end,GNCList-method Man page
end,GPos-method Man page
end<-,GRangesList-method Man page
end,GRangesList-method Man page
extractROWS,GPos-method Man page
findOverlaps Man page
findOverlaps,GenomicRanges,GenomicRanges-method Man page
findOverlaps,GenomicRanges,GRangesList-method Man page
findOverlaps,GRangesList,GenomicRanges-method Man page
findOverlaps,GRangesList,GRangesList-method Man page
findOverlaps-methods Man page
findOverlaps,RangedData,GenomicRanges-method Man page
flank Man page
flank,GenomicRanges-method Man page
flank,GRangesList-method Man page
follow Man page
follow,GenomicRanges,GenomicRanges-method Man page
follow,GenomicRanges,missing-method Man page
gaps Man page
gaps,GenomicRanges-method Man page
GenomicRanges Man page
[<-,GenomicRanges,ANY,ANY,ANY-method Man page
[,GenomicRanges,ANY-method Man page
GenomicRanges-class Man page
GenomicRanges-comparison Man page
GenomicRangesList Man page
GenomicRangesList-class Man page
$<-,GenomicRanges-method Man page
$,GenomicRanges-method Man page
GenomicRangesORGRangesList-class Man page
GenomicRangesORmissing-class Man page
genomicvariables Man page
genomicvars Man page
GNCList Man page
GNCList-class Man page
GPos Man page
GPos-class Man page
granges Man page
GRanges Man page
GRanges Man page
GRanges-class Man page
granges,GenomicRanges-method Man page
granges,GNCList-method Man page
GRangesList Man page
GRangesList Man page
[<-,GRangesList,ANY,ANY,ANY-method Man page
[[<-,GRangesList,ANY,ANY-method Man page
[<-,GRangesList,ANY-method Man page
[,GRangesList,ANY-method Man page
[[<-,GRangesList,ANY-method Man page
GRangesList-class Man page
[<-,GRangesList-method Man page
[[<-,GRangesList-method Man page
[<-,GRanges-method Man page
grglist Man page
grglist,Pairs-method Man page
inter-range-methods Man page
intersect Man page
intersect,GenomicRanges,GenomicRanges-method Man page
intersect,GenomicRanges,Vector-method Man page
intersect,GRangesList,GRangesList-method Man page
intersect,Vector,GenomicRanges-method Man page
intra-range-methods Man page
invertStrand,character-method Man page
invertStrand,factor-method Man page
invertStrand,integer-method Man page
invertStrand,logical-method Man page
invertStrand,NULL-method Man page
invertStrand,RleList-method Man page
invertStrand,Rle-method Man page
isDisjoint Man page
isDisjoint,GenomicRanges-method Man page
isDisjoint,GPos-method Man page
isDisjoint,GRangesList-method Man page
isSmallGenome Man page
is.unsorted,GenomicRanges-method Man page
length,GenomicRanges-method Man page
length,GNCList-method Man page
length,GPos-method Man page
[,list,GenomicRanges-method Man page
[,List,GenomicRanges-method Man page
makeGRangesFromDataFrame Man page
makeGRangesListFromDataFrame Man page
makeGRangesListFromFeatureFragments Man page
match,GenomicRanges,GenomicRanges-method Man page
mcolAsRleList Man page
names<-,GenomicRanges-method Man page
names,GenomicRanges-method Man page
names,GNCList-method Man page
names<-,GPos-method Man page
names,GPos-method Man page
narrow Man page
narrow,GenomicRanges-method Man page
narrow,GRangesList-method Man page
nearest Man page
nearest,GenomicRanges,GenomicRanges-method Man page
nearest,GenomicRanges,missing-method Man page
nearest-methods Man page
Ops,GenomicRanges,numeric-method Man page
order,GenomicRanges-method Man page
overlapsAny Man page
pcompare Man page
pcompare,GenomicRanges,GenomicRanges-method Man page
pgap Man page
pgap,GRanges,GRanges-method Man page
phicoef Man page
pintersect Man page
pintersect,GRanges,GRangesList-method Man page
pintersect,GRanges,GRanges-method Man page
pintersect,GRangesList,GRanges-method Man page
pos Man page
pos,GPos-method Man page
precede Man page
precede,GenomicRanges,GenomicRanges-method Man page
precede,GenomicRanges,missing-method Man page
promoters Man page
promoters,GenomicRanges-method Man page
promoters,GRangesList-method Man page
psetdiff Man page
psetdiff,GRanges,GRangesList-method Man page
psetdiff,GRanges,GRanges-method Man page
punion Man page
punion,GRanges,GRangesList-method Man page
punion,GRanges,GRanges-method Man page
punion,GRangesList,GRanges-method Man page
range Man page
range,GenomicRanges-method Man page
range,GPos-method Man page
range,GRangesList-method Man page
ranges,DelegatingGenomicRanges-method Man page
ranges<-,GenomicRanges-method Man page
ranges,GNCList-method Man page
ranges,GPos-method Man page
ranges<-,GRangesList-method Man page
ranges,GRangesList-method Man page
ranges,GRanges-method Man page
range-squeezers Man page
rank,GenomicRanges-method Man page
reduce Man page
reduce,GenomicRangesList-method Man page
reduce,GenomicRanges-method Man page
reduce,GRangesList-method Man page
relativeRanges Man page
relistToClass,GRanges-method Man page
resize Man page
resize,GenomicRanges-method Man page
resize,GRangesList-method Man page
restrict Man page
restrict,GenomicRanges-method Man page
restrict,GRangesList-method Man page
rglist Man page
rglist,Pairs-method Man page
score<-,GenomicRanges-method Man page
score,GenomicRanges-method Man page
score<-,GRangesList-method Man page
score,GRangesList-method Man page
selfmatch,GenomicRanges-method Man page
seqinfo,DelegatingGenomicRanges-method Man page
seqinfo<-,GenomicRanges-method Man page
seqinfo,GNCList-method Man page
seqinfo<-,GPos-method Man page
seqinfo,GPos-method Man page
seqinfo<-,GRangesList-method Man page
seqinfo,GRangesList-method Man page
seqinfo,GRanges-method Man page
seqinfo<-,List-method Man page
seqinfo,List-method Man page
seqinfo<-,RangedData-method Man page
seqinfo,RangedData-method Man page
seqinfo,RangesList-method Man page
seqnames,DelegatingGenomicRanges-method Man page
seqnames<-,GenomicRanges-method Man page
seqnames,GNCList-method Man page
seqnames,GPos-method Man page
seqnames<-,GRangesList-method Man page
seqnames,GRangesList-method Man page
seqnames,GRanges-method Man page
seqnames,RangedData-method Man page
setdiff Man page
setdiff,GenomicRanges,GenomicRanges-method Man page
setdiff,GenomicRanges,Vector-method Man page
setdiff,GRangesList,GRangesList-method Man page
setdiff,Vector,GenomicRanges-method Man page
setops-methods Man page
shift Man page
shift,GenomicRanges-method Man page
shift,GPos-method Man page
shift,GRangesList-method Man page
show,GenomicRanges-method Man page
show,GPos-method Man page
show,GRangesList-method Man page
SimpleGenomicRangesList-class Man page
slidingWindows Man page
slidingWindows,GenomicRanges-method Man page
sort.GenomicRanges Man page
sort,GenomicRanges-method Man page
start<-,GenomicRanges-method Man page
start,GenomicRanges-method Man page
start,GNCList-method Man page
start,GPos-method Man page
start<-,GRangesList-method Man page
start,GRangesList-method Man page
strand,character-method Man page
strand<-,DataTable,ANY-method Man page
strand,DataTable-method Man page
strand,DelegatingGenomicRanges-method Man page
strand,factor-method Man page
strand<-,GenomicRanges,ANY-method Man page
strand,GNCList-method Man page
strand,GPos-method Man page
strand<-,GRangesList,ANY-method Man page
strand<-,GRangesList,character-method Man page
strand,GRangesList-method Man page
strand,GRanges-method Man page
strand,integer-method Man page
strand,logical-method Man page
strand,missing-method Man page
strand,NULL-method Man page
strand,RleList-method Man page
strand,Rle-method Man page
strand-utils Man page
subsetByOverlaps Man page
summary.GenomicRanges Man page
summary,GenomicRanges-method Man page
tile Man page
tileGenome Man page
tile,GenomicRanges-method Man page
tile-methods Man page
trim,GenomicRanges-method Man page
union Man page
union,GenomicRanges,GenomicRanges-method Man page
union,GenomicRanges,Vector-method Man page
union,GRangesList,GRangesList-method Man page
union,Vector,GenomicRanges-method Man page
updateObject,GRangesList-method Man page
updateObject,GRanges-method Man page
width<-,GenomicRanges-method Man page
width,GenomicRanges-method Man page
width,GNCList-method Man page
width,GPos-method Man page
width<-,GRangesList-method Man page
width,GRangesList-method Man page
window,GenomicRanges-method Man page

Files

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

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