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

A pipeline for analysing Capture Hi-C data.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Chicago")
AuthorJonathan Cairns, Paula Freire Pritchett, Steven Wingett, Mikhail Spivakov
Bioconductor views Epigenetics HiC Sequencing Software
Date of publicationNone
MaintainerMikhail Spivakov <spivakov@babraham.ac.uk>
LicenseArtistic-2.0
Version1.4.0

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

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

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