Chicago: CHiCAGO: Capture Hi-C Analysis of Genomic Organization

A pipeline for analysing Capture Hi-C data.

AuthorJonathan Cairns, Paula Freire Pritchett, Steven Wingett, Mikhail Spivakov
Date of publicationNone
MaintainerMikhail Spivakov <spivakov@babraham.ac.uk>
LicenseArtistic-2.0
Version1.2.0

View on Bioconductor

Functions

cdUnitTest Man page
Chicago Man page
chicagoData Man page
Chicago-package Man page
chicagoPipeline Man page
copyCD Man page
defaultSettings Man page
estimateBrownianComponent Man page
estimateBrownianNoise Man page
estimateDistFun Man page
estimateTechnicalNoise Man page
exportResults Man page
exportToGI Man page
getPvals Man page
getScores Man page
getSkOnly Man page
intData Man page
intData<- Man page
intData<-,chicagoData-method Man page
intData,chicagoData-method Man page
mergeSamples Man page
modifySettings Man page
normaliseBaits Man page
normaliseOtherEnds Man page
overlapFragWithFeatures Man page
params Man page
params<- Man page
params<-,chicagoData-method Man page
params,chicagoData-method Man page
peakEnrichment4Features Man page
plotBaits Man page
plotDistFun Man page
readAndMerge Man page
readSample Man page
setExperiment Man page
settings Man page
settings,chicagoData-method Man page

Files

Chicago/.BBSoptions
Chicago/DESCRIPTION
Chicago/NAMESPACE
Chicago/NEWS
Chicago/R
Chicago/R/allClasses.R Chicago/R/allGenerics.R Chicago/R/chicago.R Chicago/R/chicagoData-methods.R Chicago/R/peakEnrichment4Features.R Chicago/R/zzz.R
Chicago/build
Chicago/build/vignette.rds
Chicago/data
Chicago/data/cdUnitTest.rda
Chicago/inst
Chicago/inst/CITATION
Chicago/inst/doc
Chicago/inst/doc/Chicago.R
Chicago/inst/doc/Chicago.Rmd
Chicago/inst/doc/Chicago.html
Chicago/inst/extdata
Chicago/inst/extdata/unitTestChIP
Chicago/inst/extdata/unitTestChIP/featuresmESC.txt
Chicago/inst/extdata/unitTestChIP/unitTestCTCF_ENCFF001ZQY.broadPeak.bed
Chicago/inst/extdata/unitTestChIP/unitTestH3K27me3_ENCFF001ZJO.broadPeak.bed
Chicago/inst/extdata/unitTestChIP/unitTestwgEncodeLicrHistoneEse14H3k27acME0129olaStdPk.broadPeak
Chicago/inst/extdata/unitTestChIP/unitTestwgEncodeSydhHistEse14H3k04me3StdPk.narrowPeak
Chicago/inst/extdata/unitTestChIP/unitTestwgEncodeSydhHistEse14H3k09me3StdPk.narrowPeak
Chicago/inst/extdata/unitTestData
Chicago/inst/extdata/unitTestData/unitTest_mESC_rep1.chinput
Chicago/inst/extdata/unitTestData/unitTest_mESC_rep2.chinput
Chicago/inst/extdata/unitTestDesign
Chicago/inst/extdata/unitTestDesign/unitTest.baitmap
Chicago/inst/extdata/unitTestDesign/unitTest.nbpb
Chicago/inst/extdata/unitTestDesign/unitTest.npb
Chicago/inst/extdata/unitTestDesign/unitTest.poe
Chicago/inst/extdata/unitTestDesign/unitTest.rmap
Chicago/inst/extdata/weights
Chicago/inst/extdata/weights/GM12878-2reps.settings
Chicago/inst/extdata/weights/humanMacrophage-7reps.settings
Chicago/inst/extdata/weights/mESC-2reps.settings
Chicago/man
Chicago/man/Chicago-package.Rd Chicago/man/cdUnitTest.Rd Chicago/man/chicagoData.Rd Chicago/man/chicagoPipeline.Rd Chicago/man/copyCD.Rd Chicago/man/defaultSettings.Rd Chicago/man/estimateBrownianComponent.Rd Chicago/man/estimateDistFun.Rd Chicago/man/estimateTechnicalNoise.Rd Chicago/man/exportResults.Rd Chicago/man/getPvals.Rd Chicago/man/getScores.Rd Chicago/man/getSkOnly.Rd Chicago/man/mergeSamples.Rd Chicago/man/modifySettings.Rd Chicago/man/normaliseBaits.Rd Chicago/man/normaliseOtherEnds.Rd Chicago/man/overlapFragWithFeatures.Rd Chicago/man/peakEnrichment4Features.Rd Chicago/man/plotBaits.Rd Chicago/man/plotDistFun.Rd Chicago/man/readAndMerge.Rd Chicago/man/readSample.Rd Chicago/man/setExperiment.Rd
Chicago/session.txt
Chicago/tests
Chicago/tests/testthat
Chicago/tests/testthat.R
Chicago/tests/testthat/Rplots.pdf
Chicago/tests/testthat/testRecalculateColumns.R
Chicago/tests/testthat/testRunFunctionsTwice.R
Chicago/tests/testthat/testWeights.R
Chicago/vignettes
Chicago/vignettes/Chicago.Rmd
Chicago/vignettes/Chicago.bib

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