DOI: 10.18129/B9.bioc.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 (3.15)

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")):


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biocViews Alignment, ChIPSeq, Coverage, DifferentialPeakCalling, GenomeAnnotation, Preprocessing, Sequencing, Software
Version 1.27.0
In Bioconductor since BioC 3.1 (R-3.2) (6.5 years)
License Artistic-2.0
Depends R (>= 4.0), 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 DiffBind, epigraHMM
Suggests Me
Links To Me
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