GreyListChIP
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see GreyListChIP.
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
Bioconductor version: 3.13
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 gmail.com>
Maintainer: Gordon Brown <gordon.brown at cruk.cam.ac.uk>
citation("GreyListChIP")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GreyListChIP")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GreyListChIP")| Generating Grey Lists from Input Libraries | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, ChIPSeq, Coverage, DifferentialPeakCalling, GenomeAnnotation, Preprocessing, Sequencing, Software |
| Version | 1.24.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0), methods, GenomicRanges |
| Imports | GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, GenomeInfoDb, SummarizedExperiment, stats, utils |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, BiocGenerics, RUnit |
| Linking To | |
| Enhances | BSgenome.Hsapiens.UCSC.hg19 |
| Depends On Me | |
| Imports Me | DiffBind, epigraHMM |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GreyListChIP_1.24.0.tar.gz |
| Windows Binary | GreyListChIP_1.24.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | GreyListChIP_1.24.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GreyListChIP |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GreyListChIP |
| Bioc Package Browser | https://code.bioconductor.org/browse/GreyListChIP/ |
| Package Short Url | https://bioconductor.org/packages/GreyListChIP/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.13 | Source Archive |