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genomeIntervals (version 1.28.0)

Operations on genomic intervals

Description

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'.

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Version

Version

1.28.0

License

Artistic-2.0

Maintainer

Julien Gagneur

Last Published

July 15th, 2015

Functions in genomeIntervals (1.28.0)

interval_union

Genome interval set operations
getGffAttribute

Pull one or more key/value pairs from gffAttributes strings
genomeIntervals-package

Operations on genomic intervals
gen_ints

Genome Intervals examples
readGff3,character-method

readGff3
c

c extension for the genomeIntervals package
distance_to_nearest

Distance in bases to the closest interval(s)
GenomeIntervals

Constructor function for genomeIntervals objects
Genome_intervals-class

Class "Genome\_intervals"
interval_overlap

Assess overlap from one set of genomic intervals to another
Genome_intervals_stranded-class

Class "Genome\_intervals\_stranded"
Genome_intervals-ordering

Ordering methods for Genome intervals
genomeIntervals coercion methods

Coercion methods of the genomeIntervals package
Genome_intervals deprecated functions

The following function have been deprecated:
  • seq_name
  • seq_name<-
parseGffAttributes

Parse out the gffAttributes column of a Genome\_intervals object
core_annotated

Genome intervals with minimal annotation