Package: genomeIntervals 1.61.0

Julien Gagneur

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'.

Authors:Julien Gagneur <[email protected]>, Joern Toedling, Richard Bourgon, Nicolas Delhomme

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genomeIntervals.pdf |genomeIntervals.html✨
genomeIntervals/json (API)
NEWS

# Install 'genomeIntervals' in R:

install.packages('genomeIntervals', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

i - Genome Intervals examples
j - Genome Intervals examples
k - Genome Intervals examples

On BioConductor:genomeIntervals-1.61.0(bioc 3.20)genomeIntervals-1.60.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

29 exports 2.27 score 18 dependencies 3 dependents 5 mentions

Last updated 2 months agofrom:3d5323b125

Exports:annotation annotation<-coerce core_annotated distance_to_nearest GenomeIntervals getGffAttribute inter_base inter_base<-interval_complement interval_intersection interval_overlap interval_union parseGffAttributes readBasePairFeaturesGff3 readGff3 readZeroLengthFeaturesGff3 seq_name seq_name<-seqnames seqnames<-show size strand strand<-type<-which_nearest width writeGff3

Dependencies:askpass BiocGenerics curl GenomeInfoDb GenomeInfoDbData GenomicRanges httr intervals IRanges jsonlite mime openssl R6 S4Vectors sys UCSC.utils XVector zlibbioc

Overview of the genomeIntervals package.

Rendered fromgenomeIntervals.Rnwusingutils::Sweaveon Jul 03 2024.

Last update: 2020-05-19
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Operations on genomic intervals	genomeIntervals-package genomeIntervals
c extension for the 'genomeIntervals package'	c c,Genome_intervals-method c,Genome_intervals_stranded-method
Genome intervals with minimal annotation	core_annotated core_annotated,Genome_intervals-method core_annotated,Genome_intervals_stranded-method
Distance in bases to the closest interval(s)	distance_to_nearest distance_to_nearest,Genome_intervals,Genome_intervals-method distance_to_nearest,Genome_intervals_stranded,Genome_intervals_stranded-method
Genome Intervals examples	gen_ints i j k
The following function have been deprecated: • 'seq_name' • 'seq_name<-'	Genome_intervals deprecated functions seq_name seq_name,Genome_intervals-method seq_name<- seq_name<-,Genome_intervals-method
Class "Genome\_intervals\_stranded"	coerce,Genome_intervals_stranded,character-method Genome_intervals_stranded-class strand strand,Genome_intervals_stranded-method strand<- strand<-,Genome_intervals_stranded-method
Class "Genome\_intervals"	$,Genome_intervals-method $<-,Genome_intervals-method annotation annotation,Genome_intervals-method annotation<- annotation<-,Genome_intervals-method coerce,Genome_intervals,character-method coerce,Genome_intervals,data.frame-method coerce,Genome_intervals,Intervals_full-method Genome_intervals-class inter_base inter_base,Genome_intervals-method inter_base<- inter_base<-,Genome_intervals-method seqnames,Genome_intervals-method seqnames<-,Genome_intervals-method show,Genome_intervals-method size,Genome_intervals-method strand<-,Genome_intervals_stranded,ANY-method type<-,Genome_intervals-method which_nearest,Genome_intervals,Genome_intervals-method width,Genome_intervals-method [,Genome_intervals,ANY-method [,Genome_intervals-method [<-,Genome_intervals,ANY,missing,Genome_intervals-method [[,Genome_intervals,ANY,ANY-method [[,Genome_intervals,ANY-method [[,Genome_intervals-method [[<-,Genome_intervals,ANY,ANY-method [[<-,Genome_intervals,ANY-method [[<-,Genome_intervals-method
Ordering methods for Genome intervals	Genome_intervals-ordering order order,Genome_intervals-method order,Genome_intervals_stranded-method rank rank,Genome_intervals-method rank,Genome_intervals_stranded-method sort sort,Genome_intervals-method sort,Genome_intervals_stranded-method xtfrm xtfrm,Genome_intervals-method xtfrm,Genome_intervals_stranded-method
Constructor function for genomeIntervals objects	GenomeIntervals GenomeIntervals-constructor
Coercion methods of the genomeIntervals package	as as,Genome_intervals,GRangesList-method as,Genome_intervals-method coerce,Genome_intervals,GRanges-method coerce,Genome_intervals,GRangesList-method genomeIntervals coercion methods
Pull one or more key/value pairs from gffAttributes strings	getGffAttribute
Assess overlap from one set of genomic intervals to another	interval_overlap interval_overlap,ANY,missing-method interval_overlap,Genome_intervals,Genome_intervals-method interval_overlap,Genome_intervals_stranded,Genome_intervals_stranded-method interval_overlap,missing,ANY-method
Genome interval set operations	interval_complement interval_complement,Genome_intervals-method interval_complement,Genome_intervals_stranded-method interval_intersection interval_intersection,Genome_intervals-method interval_intersection,Genome_intervals_stranded-method interval_union interval_union,Genome_intervals-method interval_union,Genome_intervals_stranded-method
Parse out the gffAttributes column of a Genome\_intervals object	parseGffAttributes
readGff3	.readGff3 readBasePairFeaturesGff3 readBasePairFeaturesGff3,character-method readGff3 readGff3,character-method readZeroLengthFeaturesGff3 readZeroLengthFeaturesGff3,character-method writeGff3 writeGff3,data.frame-method writeGff3,Genome_intervals-method