genomeIntervals: Operations on genomic intervals

This package defines classes for representing genomic intervals and provides functions and methods for working with these. Note: The package provides the basic infrastructure for and is enhanced by the package 'girafe'.

AuthorJulien Gagneur <gagneur@genzentrum.lmu.de>, Joern Toedling, Richard Bourgon, Nicolas Delhomme
Date of publicationNone
MaintainerJulien Gagneur <gagneur@genzentrum.lmu.de>
LicenseArtistic-2.0
Version1.30.0

View on Bioconductor

Functions

annotation Man page
annotation<- Man page
annotation<-,Genome_intervals-method Man page
annotation,Genome_intervals-method Man page
as Man page
as,Genome_intervals,GRangesList-method Man page
as,Genome_intervals-method Man page
as,Genome_intervals,RangedData-method Man page
c Man page
c,Genome_intervals-method Man page
c,Genome_intervals_stranded-method Man page
coerce,Genome_intervals,character-method Man page
coerce,Genome_intervals,data.frame-method Man page
coerce,Genome_intervals,GRangesList-method Man page
coerce,Genome_intervals,GRanges-method Man page
coerce,Genome_intervals,Intervals_full-method Man page
coerce,Genome_intervals,RangedData-method Man page
coerce,Genome_intervals_stranded,character-method Man page
core_annotated Man page
core_annotated,Genome_intervals-method Man page
core_annotated,Genome_intervals_stranded-method Man page
distance_to_nearest Man page
distance_to_nearest,Genome_intervals,Genome_intervals-method Man page
distance_to_nearest,Genome_intervals_stranded,Genome_intervals_s Man page
gen_ints Man page
genomeIntervals Man page
GenomeIntervals Man page
[[<-,Genome_intervals,ANY,ANY-method Man page
[[,Genome_intervals,ANY,ANY-method Man page
[,Genome_intervals,ANY-method Man page
[[<-,Genome_intervals,ANY-method Man page
[[,Genome_intervals,ANY-method Man page
[<-,Genome_intervals,ANY,missing,Genome_intervals-method Man page
Genome_intervals-class Man page
genomeIntervals coercion methods Man page
GenomeIntervals-constructor Man page
Genome_intervals deprecated functions Man page
[,Genome_intervals-method Man page
[[<-,Genome_intervals-method Man page
[[,Genome_intervals-method Man page
$<-,Genome_intervals-method Man page
$,Genome_intervals-method Man page
Genome_intervals-ordering Man page
genomeIntervals-package Man page
Genome_intervals_stranded-class Man page
getGffAttribute Man page
i Man page
inter_base Man page
inter_base<- Man page
inter_base<-,Genome_intervals-method Man page
inter_base,Genome_intervals-method Man page
interval_complement Man page
interval_complement,Genome_intervals-method Man page
interval_complement,Genome_intervals_stranded-method Man page
interval_intersection Man page
interval_intersection,Genome_intervals-method Man page
interval_intersection,Genome_intervals_stranded-method Man page
interval_overlap Man page
interval_overlap,ANY,missing-method Man page
interval_overlap,Genome_intervals,Genome_intervals-method Man page
interval_overlap,Genome_intervals_stranded,Genome_intervals_stra Man page
interval_overlap,missing,ANY-method Man page
interval_union Man page
interval_union,Genome_intervals-method Man page
interval_union,Genome_intervals_stranded-method Man page
j Man page
k Man page
order Man page
order,Genome_intervals-method Man page
order,Genome_intervals_stranded-method Man page
parseGffAttributes Man page
rank Man page
rank,Genome_intervals-method Man page
rank,Genome_intervals_stranded-method Man page
readBasePairFeaturesGff3 Man page
readBasePairFeaturesGff3,character-method Man page
readGff3 Man page
.readGff3 Man page
readGff3,character-method Man page
readZeroLengthFeaturesGff3 Man page
readZeroLengthFeaturesGff3,character-method Man page
seq_name Man page
seq_name<- Man page
seq_name<-,Genome_intervals-method Man page
seq_name,Genome_intervals-method Man page
seqnames<-,Genome_intervals-method Man page
seqnames,Genome_intervals-method Man page
show,Genome_intervals-method Man page
size,Genome_intervals-method Man page
sort Man page
sort,Genome_intervals-method Man page
sort,Genome_intervals_stranded-method Man page
strand Man page
strand<- Man page
strand<-,Genome_intervals_stranded,ANY-method Man page
strand<-,Genome_intervals_stranded-method Man page
strand,Genome_intervals_stranded-method Man page
type<-,Genome_intervals-method Man page
which_nearest,Genome_intervals,Genome_intervals-method Man page
width,Genome_intervals-method Man page
writeGff3 Man page
writeGff3,data.frame-method Man page
writeGff3,Genome_intervals-method Man page
xtfrm Man page
xtfrm,Genome_intervals-method Man page
xtfrm,Genome_intervals_stranded-method Man page

Files

genomeIntervals/DESCRIPTION
genomeIntervals/NAMESPACE
genomeIntervals/NEWS
genomeIntervals/R
genomeIntervals/R/AllGenerics.R genomeIntervals/R/Genome_intervals-class.R genomeIntervals/R/Genome_intervals-coercion-methods.R genomeIntervals/R/Genome_intervals-ordering.R genomeIntervals/R/Genome_intervals-package.R genomeIntervals/R/c.R genomeIntervals/R/core_annotated.R genomeIntervals/R/distance_to_nearest-methods.R genomeIntervals/R/interval_complement-methods.R genomeIntervals/R/interval_intersection-methods.R genomeIntervals/R/interval_overlap-methods.R genomeIntervals/R/interval_union-methods.R genomeIntervals/R/parseGffAttributes.R genomeIntervals/R/readGff3.R genomeIntervals/R/show-methods.R genomeIntervals/R/size-methods.R genomeIntervals/R/which_nearest-methods.R genomeIntervals/R/writeGff3.R
genomeIntervals/TODO.txt
genomeIntervals/build
genomeIntervals/build/vignette.rds
genomeIntervals/data
genomeIntervals/data/gen_ints.rda
genomeIntervals/inst
genomeIntervals/inst/doc
genomeIntervals/inst/doc/genomeIntervals.R
genomeIntervals/inst/doc/genomeIntervals.Rnw
genomeIntervals/inst/doc/genomeIntervals.pdf
genomeIntervals/inst/example_files
genomeIntervals/inst/example_files/sgd_simple.gff
genomeIntervals/man
genomeIntervals/man/GenomeIntervals-constructor.Rd genomeIntervals/man/Genome_intervals-class.Rd genomeIntervals/man/Genome_intervals-coercion-methods.Rd genomeIntervals/man/Genome_intervals-deprecated.Rd genomeIntervals/man/Genome_intervals-ordering.Rd genomeIntervals/man/Genome_intervals_stranded-class.Rd genomeIntervals/man/c.Genome_intervals.Rd genomeIntervals/man/core_annotated.Rd genomeIntervals/man/distance_to_nearest-methods.Rd genomeIntervals/man/gen_ints.Rd genomeIntervals/man/genomeIntervals-package.Rd genomeIntervals/man/genomeIntervals-readGff3.Rd genomeIntervals/man/getGffAttribute.Rd genomeIntervals/man/interval_overlap-methods.Rd genomeIntervals/man/interval_set_operations-methods.Rd genomeIntervals/man/parseGffAttributes.Rd
genomeIntervals/script
genomeIntervals/script/makeData.R
genomeIntervals/tests
genomeIntervals/tests/benchmarking-tests.R
genomeIntervals/tests/benchmarking-tests.Rout.save
genomeIntervals/tests/consistency-tests.R
genomeIntervals/tests/fullShow.R
genomeIntervals/vignettes
genomeIntervals/vignettes/genomeIntervals.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.