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Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Bioconductor version: Release (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>

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


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

if (!require("BiocManager", quietly = TRUE))


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


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews Alignment, ChIPSeq, Coverage, DifferentialPeakCalling, GenomeAnnotation, Preprocessing, Sequencing, Software
Version 1.36.0
In Bioconductor since BioC 3.1 (R-3.2) (9.5 years)
License Artistic-2.0
Depends R (>= 4.0), methods, GenomicRanges
Imports GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, GenomeInfoDb, SummarizedExperiment, stats, utils
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Suggests BiocStyle, BiocGenerics, RUnit, BSgenome.Hsapiens.UCSC.hg19
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Imports Me DiffBind, epigraHMM
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Follow Installation instructions to use this package in your R session.

Source Package GreyListChIP_1.36.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) GreyListChIP_1.36.0.tgz
macOS Binary (arm64) GreyListChIP_1.36.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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