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
| Maintainer | Matt Eldridge <matthew.eldridge@cruk.cam.ac.uk> |
| Author | Matt Eldridge [cre], Gord Brown [aut] |
| License | Artistic-2.0 |
| Downloads rank | 1607 |
| Source branch | RELEASE_3_23 |
| biocViews | Alignment, ChIPSeq, Coverage, DifferentialPeakCalling, GenomeAnnotation, Preprocessing, Sequencing, Software |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | GreyListChIP_1.44.0.tar.gz |
| Windows binary (x86_64) | GreyListChIP_1.44.0.zip |
| macOS binary (arm64) | GreyListChIP_1.44.0.tgz |
| macOS binary (x86_64) | GreyListChIP_1.44.0.tgz |
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