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GreyListChIP (version 1.4.0)

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Description

Identify regions of ChIP experiments with high signal in the input, that lead to spurious peaks during peak calling. Remove reads aligning to these regions prior to peak calling, for cleaner ChIP analysis.

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Version

Version

1.4.0

License

Artistic-2.0

Maintainer

Gordon Brown

Last Published

February 15th, 2017

Functions in GreyListChIP (1.4.0)

countReads-methods

Count reads from a BamFile
loadKaryotype-methods

Load a karyotype from a file
GreyList-class

"GreyList" Objects
calcThreshold-methods

Calculate Read Count Threshold
greyList

A sample GreyList object for use in examples.
greyListBS

Construct a grey list with default arguments
getKaryotype-methods

Replace the karyotype of a GreyList object
makeGreyList-methods

Generate a grey list from a GreyList object