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GreyListChIP

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Bioconductor version: 3.23 · Package version: 1.44.0

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.

Installation

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

BiocManager::install("GreyListChIP")

Details

MaintainerMatt Eldridge <matthew.eldridge@cruk.cam.ac.uk>
AuthorMatt Eldridge [cre], Gord Brown [aut]
LicenseArtistic-2.0
Downloads rank1429
Source branchRELEASE_3_23
biocViewsAlignment, ChIPSeq, Coverage, DifferentialPeakCalling, GenomeAnnotation, Preprocessing, Sequencing, Software

Documentation

Download

Dependencies

Depends: R (>= 4.0), methods, GenomicRanges

Imports: GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, Seqinfo, SummarizedExperiment, stats, utils

Suggests: BiocStyle, BiocGenerics, RUnit, BSgenome.Hsapiens.UCSC.hg19

Reverse dependencies

Imports Me (2): DiffBind, epigraHMM