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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

License

Artistic-2.0

Maintainer

Mikhail Spivakov

Last Published

February 15th, 2017

Functions in Chicago (1.0.3)

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