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

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

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