GenomicTuples: Representation and Manipulation of Genomic Tuples

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GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges Bioconductor package.

Author
Peter Hickey <peter.hickey@gmail.com>, with contributions from Marcin Cieslik and Herve Pages.
Date of publication
None
Maintainer
Peter Hickey <peter.hickey@gmail.com>
License
Artistic-2.0
Version
1.8.1
URLs

View on Bioconductor

Man pages

findOverlaps-methods
Finding overlapping genomic tuples
GenomicTuples-package
Representation and manipulation of genomic tuples.
GTuples-class
GTuples objects
GTuples-comparison
Comparing and ordering genomic tuples
GTuplesList-class
GTuplesList objects
illdefined-methods
Undefined methods
intra-tuple-methods
Intra-tuple transformations of a GTuples or GTuplesLists...
nearest-methods
Finding the nearest genomic tuple/range neighbour
tuples-squeezers
Squeeze the tuples out of a tuples-based object

Files in this package

GenomicTuples/DESCRIPTION
GenomicTuples/NAMESPACE
GenomicTuples/R
GenomicTuples/R/AllGenerics.R
GenomicTuples/R/AllUtilities.R
GenomicTuples/R/GTuples-class.R
GenomicTuples/R/GTuples-comparison.R
GenomicTuples/R/GTuplesList-class.R
GenomicTuples/R/GenomicTuples.R
GenomicTuples/R/RcppExports.R
GenomicTuples/R/coverage-methods.R
GenomicTuples/R/findOverlaps-methods.R
GenomicTuples/R/inter-tuple-methods.R
GenomicTuples/R/intra-tuple-methods.R
GenomicTuples/R/nearest-methods.R
GenomicTuples/R/setops-methods.R
GenomicTuples/R/tile-methods.R
GenomicTuples/R/zzz.R
GenomicTuples/README.md
GenomicTuples/build
GenomicTuples/build/vignette.rds
GenomicTuples/inst
GenomicTuples/inst/CITATION
GenomicTuples/inst/NEWS.Rd
GenomicTuples/inst/doc
GenomicTuples/inst/doc/GenomicTuplesIntroduction.R
GenomicTuples/inst/doc/GenomicTuplesIntroduction.Rmd
GenomicTuples/inst/doc/GenomicTuplesIntroduction.html
GenomicTuples/man
GenomicTuples/man/GTuples-class.Rd
GenomicTuples/man/GTuples-comparison.Rd
GenomicTuples/man/GTuplesList-class.Rd
GenomicTuples/man/GenomicTuples-package.Rd
GenomicTuples/man/findOverlaps-methods.Rd
GenomicTuples/man/illdefined-methods.Rd
GenomicTuples/man/intra-tuple-methods.Rd
GenomicTuples/man/nearest-methods.Rd
GenomicTuples/man/tuples-squeezers.Rd
GenomicTuples/src
GenomicTuples/src/GenomicTuples_init.c
GenomicTuples/src/IPD.cpp
GenomicTuples/src/RcppExports.cpp
GenomicTuples/src/allTuplesSorted.cpp
GenomicTuples/src/pcompareGTuples.cpp
GenomicTuples/tests
GenomicTuples/tests/testthat
GenomicTuples/tests/testthat.R
GenomicTuples/tests/testthat/helper-make-test-data.R
GenomicTuples/tests/testthat/test-AllUtilities.R
GenomicTuples/tests/testthat/test-GTuples-class.R
GenomicTuples/tests/testthat/test-GTuples-comparison.R
GenomicTuples/tests/testthat/test-GTuplesList-class.R
GenomicTuples/tests/testthat/test-coverage-methods.R
GenomicTuples/tests/testthat/test-findOverlaps-methods.R
GenomicTuples/tests/testthat/test-inter-tuple-methods.R
GenomicTuples/tests/testthat/test-intra-tuple-methods.R
GenomicTuples/tests/testthat/test-nearest-methods.R
GenomicTuples/tests/testthat/test-setops-methods.R
GenomicTuples/tests/testthat/test-tile-methods.R
GenomicTuples/vignettes
GenomicTuples/vignettes/GenomicTuplesIntroduction.Rmd