- Home
- Bioconductor 3.5
- Software Packages
- GreyListChIP
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
|
|
|
|
|
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")
| R Script | Generating Grey Lists from Input Libraries | |
| 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.
| Source Package | 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 |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
