GreyListChIP
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
Bioconductor version: 3.23 · Package version: 1.44.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, ChIPSeq, Coverage, DifferentialPeakCalling, GenomeAnnotation, Preprocessing, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/GreyListChIP/ |
Citation
From within R, enter citation("GreyListChIP"):
Gord Brown. GreyListChIP: Grey Lists -- Mask Artefact Regions Based on ChIP Inputs. doi:10.18129/B9.bioc.GreyListChIP, R package version 1.44.0, https://bioconductor.org/packages/GreyListChIP.
Generated from the package metadata; it may differ from the package's own citation.
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