GenomicInteractions: R package for handling genomic interaction data

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R package for handling Genomic interaction data, such as ChIA-PET/Hi-C, annotating genomic features with interaction information and producing various plots / statistics.

Author
Harmston, N., Ing-Simmons, E., Perry, M., Baresic, A., Lenhard, B.
Date of publication
None
Maintainer
Malcolm Perry <mgperry32@gmail.com>, Liz Ing-Simmons <liz.ing-simmons12@csc.mrc.ac.uk>
License
GPL-3
Version
1.8.0
URLs

View on Bioconductor

Man pages

annotateAnchors
Annotate anchors - DEPRECATED
annotateInteractions
Annotate the interactions in a GInteractions object
annotateRegions
Annotate regions
asBED-GInteractions-method
Coerce to BED structure
availableDisplayPars
The default display parameters for a track object class can...
calculateDistances
Calculate interaction distances
categoriseInteractions
Get the numbers of interaction types existing in your data
countsBetweenAnchors-methods
Summarise interactions between defined anchors
export.bed12
Export interactions in BED12 format.
export.bedpe
Export interactions in BED Paired-End format.
export.chiasig
Export interactions in a BEDPE-like format for use with...
export.igraph
Export interactions to an igraph object.
GenomicInteractions
Function to create a GenomicInteractions object
GenomicInteractions-class
A S4 class to represent interactions between genomic regions.
GenomicInteractions-package
A package for looking at genomic interaction data.
get_binom_ligation_threshold
get self ligation threshold with binomial test
get_self_ligation_threshold
Get self ligation threshold with SD method from Heidari et al
getters
Functions to access data held in a GenomicInteractions...
GInteractions-subsetByFeatures-methods
Subset a GInteractions object by features
hg19.refseq.transcripts
Human Refseq transcripts from chr 17-18
hic_example_data
Example HiC dataset
InteractionHelpers
Interaction Type Helpers
InteractionTrack
Constructor to create an InteractionTrack object
InteractionTrack-class
A class to hold chromatin interaction data for a specific...
makeGenomicInteractionsFromFile
Function to create GenomicInteraction objects from a file
mm9_refseq_promoters
Mouse Refseq promoters from chr 14-15
plotAvgViewpoint
Plot coverage around a set of virtual 4C viewpoints
plotCisTrans
Plots the percentages of cis and trans interactions for a...
plotCounts
Plot a bar chart of the number of interactions supported by...
plotDists
Plots a histogram of interaction distances for a...
plotInteractionAnnotations
Plot a donut plot of interaction types for an annotated...
plotSummaryStats
Plot summary statistics for a GInteractions object
plotViewpoint
Plot coverage around a virtual 4C viewpoint
removeDups
Remove all but one occurences of a duplicated interaction
resetAnnotations
Reset annotations made to a GInteractions object
sameStrand
Tests whether anchors have the same strand.
setters
Functions to set data held in a GInteractions object.
sum-GInteractions-method
Return the total number of interactions in a GInteractions...
summariseByFeaturePairs
Summarise the number of interactions between two sets of...
summariseByFeatures
Summary statistics of interactions for a given feature set
thymus_enh
Putative enhancers from mouse thymus data
updateObject-GenomicInteractions-method
updateObject method for GenomicInteractions 1.3.7 and earlier
viewPoint
Virtual 4C viewpoint

Files in this package

GenomicInteractions/DESCRIPTION
GenomicInteractions/NAMESPACE
GenomicInteractions/NEWS
GenomicInteractions/R
GenomicInteractions/R/DocumentData.R
GenomicInteractions/R/GenomicInteractions-class.R
GenomicInteractions/R/GenomicInteractions-package.R
GenomicInteractions/R/InteractionTrack-class.R
GenomicInteractions/R/annotators.R
GenomicInteractions/R/calculateDistances.R
GenomicInteractions/R/export.R
GenomicInteractions/R/export.igraph.R
GenomicInteractions/R/getters.R
GenomicInteractions/R/helpers.R
GenomicInteractions/R/import.R
GenomicInteractions/R/library.R
GenomicInteractions/R/plotSummaryStats.R
GenomicInteractions/R/processing.R
GenomicInteractions/R/setters.R
GenomicInteractions/R/subsetting.R
GenomicInteractions/R/summarise_annotations.r
GenomicInteractions/R/viewPoints.R
GenomicInteractions/README.md
GenomicInteractions/build
GenomicInteractions/build/vignette.rds
GenomicInteractions/data
GenomicInteractions/data/hg19.refseq.transcripts.rda
GenomicInteractions/data/hic_example_data.rda
GenomicInteractions/data/mm9_refseq_promoters.rda
GenomicInteractions/data/thymus_enhancers.rda
GenomicInteractions/inst
GenomicInteractions/inst/doc
GenomicInteractions/inst/doc/chiapet_vignette.R
GenomicInteractions/inst/doc/chiapet_vignette.html
GenomicInteractions/inst/doc/chiapet_vignette.rmd
GenomicInteractions/inst/doc/hic_vignette.R
GenomicInteractions/inst/doc/hic_vignette.Rmd
GenomicInteractions/inst/doc/hic_vignette.html
GenomicInteractions/inst/extdata
GenomicInteractions/inst/extdata/Seitan2013_WT_100kb_interactions.txt
GenomicInteractions/inst/extdata/k562.rep1.cluster.pet3+.txt
GenomicInteractions/man
GenomicInteractions/man/GInteractions-subsetByFeatures-methods.Rd
GenomicInteractions/man/GenomicInteractions-class.Rd
GenomicInteractions/man/GenomicInteractions-package.Rd
GenomicInteractions/man/GenomicInteractions.Rd
GenomicInteractions/man/InteractionHelpers.Rd
GenomicInteractions/man/InteractionTrack-class.Rd
GenomicInteractions/man/InteractionTrack.Rd
GenomicInteractions/man/annotateAnchors.Rd
GenomicInteractions/man/annotateInteractions.Rd
GenomicInteractions/man/annotateRegions.Rd
GenomicInteractions/man/asBED-GInteractions-method.Rd
GenomicInteractions/man/availableDisplayPars.Rd
GenomicInteractions/man/calculateDistances.Rd
GenomicInteractions/man/categoriseInteractions.Rd
GenomicInteractions/man/countsBetweenAnchors-methods.Rd
GenomicInteractions/man/export.bed12.Rd
GenomicInteractions/man/export.bedpe.Rd
GenomicInteractions/man/export.chiasig.Rd
GenomicInteractions/man/export.igraph.Rd
GenomicInteractions/man/get_binom_ligation_threshold.Rd
GenomicInteractions/man/get_self_ligation_threshold.Rd
GenomicInteractions/man/getters.Rd
GenomicInteractions/man/hg19.refseq.transcripts.Rd
GenomicInteractions/man/hic_example_data.Rd
GenomicInteractions/man/makeGenomicInteractionsFromFile.Rd
GenomicInteractions/man/mm9_refseq_promoters.Rd
GenomicInteractions/man/plotAvgViewpoint.Rd
GenomicInteractions/man/plotCisTrans.Rd
GenomicInteractions/man/plotCounts.Rd
GenomicInteractions/man/plotDists.Rd
GenomicInteractions/man/plotInteractionAnnotations.Rd
GenomicInteractions/man/plotSummaryStats.Rd
GenomicInteractions/man/plotViewpoint.Rd
GenomicInteractions/man/removeDups.Rd
GenomicInteractions/man/resetAnnotations.Rd
GenomicInteractions/man/sameStrand.Rd
GenomicInteractions/man/setters.Rd
GenomicInteractions/man/sum-GInteractions-method.Rd
GenomicInteractions/man/summariseByFeaturePairs.Rd
GenomicInteractions/man/summariseByFeatures.Rd
GenomicInteractions/man/thymus_enh.Rd
GenomicInteractions/man/updateObject-GenomicInteractions-method.Rd
GenomicInteractions/man/viewPoint.Rd
GenomicInteractions/tests
GenomicInteractions/tests/testthat
GenomicInteractions/tests/testthat.R
GenomicInteractions/tests/testthat/test_annotation.R
GenomicInteractions/tests/testthat/test_getters.R
GenomicInteractions/tests/testthat/test_import.R
GenomicInteractions/tests/testthat/test_summarystats.R
GenomicInteractions/tests/testthat/test_valid.R
GenomicInteractions/vignettes
GenomicInteractions/vignettes/chiapet_vignette.rmd
GenomicInteractions/vignettes/hic_vignette.Rmd