DOI: 10.18129/B9.bioc.GreyListChIP    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see GreyListChIP.

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Bioconductor version: 3.8

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>

Maintainer: Gordon Brown <gordon.brown at>

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


To install this package, start R (version "3.5") and enter:

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

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


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PDF R Script Generating Grey Lists from Input Libraries
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biocViews Alignment, ChIPSeq, Coverage, DifferentialPeakCalling, GenomeAnnotation, Preprocessing, Sequencing, Software
Version 1.14.0
In Bioconductor since BioC 3.1 (R-3.2) (4 years)
License Artistic-2.0
Depends R (>= 3.5), methods, GenomicRanges
Imports GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, GenomeInfoDb, SummarizedExperiment, stats, utils
Suggests BiocStyle, BiocGenerics, RUnit
Enhances BSgenome.Hsapiens.UCSC.hg19
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package GreyListChIP_1.14.0.tar.gz
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