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Chicago (version 1.0.3)
CHiCAGO: Capture Hi-C Analysis of Genomic Organization
Description
A pipeline for analysing Capture Hi-C data.
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Version
Version
1.0.3
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Version
1.0.3
License
Artistic-2.0
Maintainer
Mikhail Spivakov
Last Published
January 1st, 1970
Functions in Chicago (1.0.3)
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chicagoPipeline
CHiCAGO pipeline function
estimateDistFun
Estimate the Distance Function
plotDistFun
Plot the Distance Function
getPvals
Get P-values
setExperiment
Set Experiment
cdUnitTest
ChicagoData object for unit testing
readSample
Read Sample
getScores
Get CHiCAGO scores.
mergeSamples
Merge samples together.
chicagoData
The
chicagoData
class.
overlapFragWithFeatures
Overlap Other-Ends with Features
getSkOnly
Get S_k factors from multiple replicates
Chicago-package
CHiCAGO: Capture Hi-C Analysis of Genomic Organization
normaliseBaits
Normalise Baits
estimateBrownianComponent
Estimate Brownian background component.
exportResults
Export Results
plotBaits
Plot Baits
peakEnrichment4Features
Enrichment for Features
modifySettings
Modify Settings
defaultSettings
Default CHiCAGO settings
copyCD
Copy chicagoData object
estimateTechnicalNoise
Estimate Technical Noise
normaliseOtherEnds
Normalise Other Ends
readAndMerge
Read And Merge