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GreyListChIP

This is the development version of GreyListChIP; for the stable release version, see GreyListChIP.

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs


Bioconductor version: Development (3.19)

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: Matt Eldridge [cre], Gord Brown [aut]

Maintainer: Matt Eldridge <matthew.eldridge at cruk.cam.ac.uk>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Alignment, ChIPSeq, Coverage, DifferentialPeakCalling, GenomeAnnotation, Preprocessing, Sequencing, Software
Version 1.35.1
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License Artistic-2.0
Depends R (>= 4.0), methods, GenomicRanges
Imports GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, GenomeInfoDb, SummarizedExperiment, stats, utils
System Requirements
URL
See More
Suggests BiocStyle, BiocGenerics, RUnit, BSgenome.Hsapiens.UCSC.hg19
Linking To
Enhances
Depends On Me
Imports Me DiffBind, epigraHMM
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package GreyListChIP_1.35.1.tar.gz
Windows Binary GreyListChIP_1.35.1.zip (64-bit only)
macOS Binary (x86_64) GreyListChIP_1.35.1.tgz
macOS Binary (arm64) GreyListChIP_1.35.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/GreyListChIP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GreyListChIP
Bioc Package Browser https://code.bioconductor.org/browse/GreyListChIP/
Package Short Url https://bioconductor.org/packages/GreyListChIP/
Package Downloads Report Download Stats