- Home
- Bioconductor 3.22
- Software Packages
- GreyListChIP
GreyListChIP
This is thereleased version of GreyListChIP; for the devel version, seeGreyListChIP.
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
Bioconductor version: Release (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("GreyListChIP")For older versions of R, please refer to the appropriateBioconductor 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 | 1.42.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (10.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0), methods,GenomicRanges |
| Imports | GenomicAlignments,BSgenome,Rsamtools,rtracklayer,MASS, parallel,Seqinfo,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
FollowInstallation instructions to use this package in your R session.
| Source Package | GreyListChIP_1.42.0.tar.gz |
| Windows Binary (x86_64) | GreyListChIP_1.42.0.zip (64-bit only) |
| macOS Binary (x86_64) | GreyListChIP_1.42.0.tgz |
| macOS Binary (arm64) | GreyListChIP_1.42.0.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 |