genomeIntervals: Operations on genomic intervals

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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'.

Author
Julien Gagneur <gagneur@genzentrum.lmu.de>, Joern Toedling, Richard Bourgon, Nicolas Delhomme
Date of publication
None
Maintainer
Julien Gagneur <gagneur@genzentrum.lmu.de>
License
Artistic-2.0
Version
1.30.0

View on Bioconductor

Man pages

c.Genome_intervals
c extension for the 'genomeIntervals package'
core_annotated
Genome intervals with minimal annotation
distance_to_nearest-methods
Distance in bases to the closest interval(s)
gen_ints
Genome Intervals examples
Genome_intervals-class
Class "Genome\_intervals"
Genome_intervals-coercion-methods
Coercion methods of the genomeIntervals package
GenomeIntervals-constructor
Constructor function for genomeIntervals objects
Genome_intervals-deprecated
The following function have been deprecated: • 'seq_name' •...
Genome_intervals-ordering
Ordering methods for Genome intervals
genomeIntervals-package
Operations on genomic intervals
genomeIntervals-readGff3
readGff3
Genome_intervals_stranded-class
Class "Genome\_intervals\_stranded"
getGffAttribute
Pull one or more key/value pairs from gffAttributes strings
interval_overlap-methods
Assess overlap from one set of genomic intervals to another
interval_set_operations-methods
Genome interval set operations
parseGffAttributes
Parse out the gffAttributes column of a Genome\_intervals...

Files in this package

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