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

DOI: 10.18129/B9.bioc.GreyListChIP    

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Bioconductor version: Release (3.5)

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 R Script Generating Grey Lists from Input Libraries
PDF   Reference Manual
Text   NEWS

Details

biocViews Alignment, ChIPSeq, Coverage, DifferentialPeakCalling, GenomeAnnotation, Preprocessing, Sequencing, Software
Version 1.8.0
In Bioconductor since BioC 3.1 (R-3.2) (2.5 years)
License Artistic-2.0
Depends R (>= 3.1), methods, GenomicRanges
Imports GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, GenomeInfoDb, SummarizedExperiment, stats, utils
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_1.8.0.tar.gz
Windows Binary GreyListChIP_1.8.0.zip
Mac OS X 10.11 (El Capitan) GreyListChIP_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GreyListChIP
Package Short Url http://bioconductor.org/packages/GreyListChIP/
Package Downloads Report Download Stats

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