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'.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("genomeIntervals")
AuthorJulien Gagneur <gagneur@genzentrum.lmu.de>, Joern Toedling, Richard Bourgon, Nicolas Delhomme
Bioconductor views DataImport Genetics Infrastructure
Date of publicationNone
MaintainerJulien Gagneur <gagneur@genzentrum.lmu.de>
LicenseArtistic-2.0
Version1.32.0

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

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

Please suggest features or report bugs with the GitHub issue tracker.

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