ChIPComp
This is the development version of ChIPComp; for the stable release version, see ChIPComp.
Quantitative comparison of multiple ChIP-seq datasets
Bioconductor version: Development (3.24)
ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control.
Author: Hao Wu, Li Chen, Zhaohui S.Qin, Chi Wang
Maintainer: Li Chen <li.chen at emory.edu>
citation("ChIPComp")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("ChIPComp")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | ChIPSeq, Coverage, DataImport, Genetics, MultipleComparison, Sequencing, Software, Transcription |
| Version | 1.43.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 years) |
| License | GPL |
| Depends | R (>= 3.2.0), GenomicRanges, IRanges, rtracklayer, Seqinfo, S4Vectors |
| Imports | Rsamtools, limma, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9, BiocGenerics |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, RUnit |
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| Depends On Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/ChIPComp |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ChIPComp |
| Package Short Url | https://bioconductor.org/packages/ChIPComp/ |
| Package Downloads Report | Download Stats |