GreyListChIP

DOI: 10.18129/B9.bioc.GreyListChIP    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see GreyListChIP.

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Bioconductor version: 3.14

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GreyListChIP")

For older versions of R, please refer to the appropriate Bioconductor release.

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	1.26.0
In Bioconductor since	BioC 3.1 (R-3.2) (7 years)
License	Artistic-2.0
Depends	R (>= 4.0), 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	DiffBind, epigraHMM
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	GreyListChIP_1.26.0.tar.gz
Windows Binary	GreyListChIP_1.26.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	GreyListChIP_1.26.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GreyListChIP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GreyListChIP
Package Short Url	https://bioconductor.org/packages/GreyListChIP/
Package Downloads Report	Download Stats