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

Share:

A pipeline for analysing Capture Hi-C data.

Author
Jonathan Cairns, Paula Freire Pritchett, Steven Wingett, Mikhail Spivakov
Date of publication
None
Maintainer
Mikhail Spivakov <spivakov@babraham.ac.uk>
License
Artistic-2.0
Version
1.2.0

View on Bioconductor

Man pages

cdUnitTest
ChicagoData object for unit testing
chicagoData
The 'chicagoData' class.
Chicago-package
CHiCAGO: Capture Hi-C Analysis of Genomic Organization
chicagoPipeline
CHiCAGO pipeline function
copyCD
Copy chicagoData object
defaultSettings
Default CHiCAGO settings
estimateBrownianComponent
Estimate Brownian background component.
estimateDistFun
Estimate the Distance Function
estimateTechnicalNoise
Estimate Technical Noise
exportResults
Export Results
getPvals
Get P-values
getScores
Get CHiCAGO scores.
getSkOnly
Get S_k factors from multiple replicates
mergeSamples
Merge samples together.
modifySettings
Modify Settings
normaliseBaits
Normalise Baits
normaliseOtherEnds
Normalise Other Ends
overlapFragWithFeatures
Overlap Other-Ends with Features
peakEnrichment4Features
Enrichment for Features
plotBaits
Plot Baits
plotDistFun
Plot the Distance Function
readAndMerge
Read And Merge
readSample
Read Sample
setExperiment
Set Experiment

Files in this package

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