GenomicInteractions: R package for handling genomic interaction data

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

AuthorHarmston, N., Ing-Simmons, E., Perry, M., Baresic, A., Lenhard, B.
Date of publicationNone
MaintainerMalcolm Perry <mgperry32@gmail.com>, Liz Ing-Simmons <liz.ing-simmons12@csc.mrc.ac.uk>
LicenseGPL-3
Version1.8.1
https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/

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: GenomicInteractions: A package for analysing chromosome...

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

Functions

anchorOne Man page
anchorOne,GInteractions-method Man page
anchorTwo Man page
anchorTwo,GInteractions-method Man page
annotateAnchors Man page
annotateAnchors,GenomicInteractions,numeric,character,vector-met Man page
annotateInteractions Man page
annotateInteractions,GInteractions,list-method Man page
annotateRegions Man page
annotateRegions,GInteractions,character,vector-method Man page
annotationFeatures Man page
annotationFeatures,GInteractions-method Man page
asBED,GInteractions-method Man page
availableDisplayPars Man page
calculateDistances Man page
calculateDistances,GInteractions-method Man page
categoriseInteractions Man page
countsBetweenAnchors Man page
countsBetweenAnchors,GInteractions,GRanges-method Man page
description<-,GInteractions,ANY-method Man page
description,GInteractions-method Man page
export.bed12 Man page
export.bed12,GInteractions-method Man page
export.bedpe Man page
export.bedpe,GInteractions-method Man page
export.chiasig Man page
export.chiasig,GInteractions-method Man page
export.igraph Man page
export.igraph,GInteractions-method Man page
GenomicInteractions Man page
GenomicInteractions,ANY,ANY,ANY-method Man page
GenomicInteractions-class Man page
GenomicInteractions,GInteractions,ANY,ANY-method Man page
GenomicInteractions,GInteractions,numeric,ANY-method Man page
GenomicInteractions,GRanges,GRanges,GenomicRangesORmissing-metho Man page
GenomicInteractions,GRanges,GRanges,numeric-method Man page
GenomicInteractions,missing,missing,GenomicRangesORmissing-metho Man page
GenomicInteractions,numeric,numeric,GRanges-method Man page
GenomicInteractions-package Man page
get_binom_ligation_threshold Man page
get_self_ligation_threshold Man page
getters Man page
hg19.refseq.transcripts Man page
hic_example_data Man page
interactionCounts Man page
interactionCounts<- Man page
interactionCounts<-,GInteractions-method Man page
interactionCounts,GInteractions-method Man page
InteractionHelpers Man page
InteractionTrack Man page
InteractionTrack-class Man page
is.cis Man page
is.cis,GInteractions-method Man page
is.dd Man page
is.dd,GInteractions-method Man page
is.dt Man page
is.dt,GInteractions-method Man page
isInteractionType Man page
isInteractionType,GInteractions-method Man page
is.pd Man page
is.pd,GInteractions-method Man page
is.pp Man page
is.pp,GInteractions-method Man page
is.pt Man page
is.pt,GInteractions-method Man page
is.trans Man page
is.trans,GInteractions-method Man page
is.tt Man page
is.tt,GInteractions-method Man page
makeGenomicInteractionsFromFile Man page
mm9_refseq_promoters Man page
name Man page
name<- Man page
name<-,GInteractions-method Man page
name,GInteractions-method Man page
plotAvgViewpoint Man page
plotCisTrans Man page
plotCounts Man page
plotDists Man page
plotInteractionAnnotations Man page
plotSummaryStats Man page
plotViewpoint Man page
removeDups Man page
resetAnnotations Man page
resetAnnotations,GInteractions-method Man page
sameStrand Man page
setters Man page
subsetByFeatures Man page
subsetByFeatures,GInteractions,character,character-method Man page
subsetByFeatures,GInteractions,GRangesList,missing-method Man page
subsetByFeatures,GInteractions,GRanges,missing-method Man page
sum,GInteractions-method Man page
summariseByFeaturePairs Man page
summariseByFeaturePairs,GInteractions-method Man page
summariseByFeatures Man page
summariseByFeatures,GInteractions-method Man page
thymus_enh Man page
updateObject,GenomicInteractions-method Man page
viewPoint Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.