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

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

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