To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GreyListChIP")

In most cases, you don't need to download the package archive at all.

GreyListChIP

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see GreyListChIP.

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Bioconductor version: 3.2

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.

Author: Gord Brown <gdbzork at gmail.com>

Maintainer: Gordon Brown <gordon.brown at cruk.cam.ac.uk>

Citation (from within R, enter citation("GreyListChIP")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GreyListChIP")

Documentation

To view documentation for the version of this package installed in your system, start R and enter: 

browseVignettes("GreyListChIP")
PDF Generating Grey Lists from Input Libraries
PDF Reference Manual
Text NEWS

Details

biocViews Alignment, ChIPSeq, Coverage, DifferentialPeakCalling, GenomeAnnotation, Preprocessing, Sequencing, Software
Version 1.2.0
In Bioconductor since BioC 3.1 (R-3.2) (1 year)
License Artistic-2.0
Depends R (>= 3.1), methods, GenomicRanges
Imports GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, GenomeInfoDb
LinkingTo
Suggests BiocStyle, BiocGenerics, RUnit
SystemRequirements
Enhances BSgenome.Hsapiens.UCSC.hg19
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source GreyListChIP_1.2.0.tar.gz
Windows Binary GreyListChIP_1.2.0.zip
Mac OS X 10.6 (Snow Leopard) GreyListChIP_1.2.0.tgz
Mac OS X 10.9 (Mavericks) GreyListChIP_1.2.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/GreyListChIP/tree/release-3.2
Package Short Url http://bioconductor.org/packages/GreyListChIP/
Package Downloads Report Download Stats

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