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 (3.19)
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: Matt Eldridge [cre], Gord Brown [aut]
Maintainer: Matt Eldridge <matthew.eldridge at cruk.cam.ac.uk>
Citation (from within R, enter
citation("GreyListChIP")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("GreyListChIP")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Alignment, ChIPSeq, Coverage, DifferentialPeakCalling, GenomeAnnotation, Preprocessing, Sequencing, Software |
| Version | 1.35.1 |
| 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, BSgenome.Hsapiens.UCSC.hg19 |
| Linking To | |
| Enhances | |
| 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 | |
| Windows Binary | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/GreyListChIP |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GreyListChIP |
| Package Short Url | https://bioconductor.org/packages/GreyListChIP/ |
| Package Downloads Report | Download Stats |