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To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("GreyListChIP")
In most cases, you don't need to download the package archive at all.
GreyListChIP
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
Bioconductor version: 3.1
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 is not available
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")
| R Script | Generating Grey Lists from Input Libraries | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Alignment, ChIPSeq, Coverage, DifferentialPeakCalling, GenomeAnnotation, Preprocessing, Sequencing, Software |
| Version | 1.0.1 |
| In Bioconductor since | BioC 3.1 (R-3.2) (< 6 months) |
| 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_1.0.1.tar.gz |
| Windows Binary | GreyListChIP_1.0.1.zip |
| Mac OS X 10.6 (Snow Leopard) | GreyListChIP_1.0.1.tgz |
| Mac OS X 10.9 (Mavericks) | GreyListChIP_1.0.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/GreyListChIP/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/GreyListChIP/ |
| Package Downloads Report | Download Stats |
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