ChIPexoQualExample
This is the released version of ChIPexoQualExample; for the devel version, see ChIPexoQualExample.
Example data for the ChIPexoQual package, which implements a quality control pipeline for ChIP-exo data
Bioconductor version: Release (3.23)
Data for the ChIPexoQual package, consisting of (3) chromosome 1 aligned reads from a ChIP-exo experiment for FoxA1 in mouse liver cell lines aligned to the mm9 genome.
Author: Rene Welch, Dongjun Chung, Sunduz Keles
Maintainer: Rene Welch <welch at stat.wisc.edu>
citation("ChIPexoQualExample")):
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")
BiocManager::install("ChIPexoQualExample")
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("ChIPexoQualExample")| ChIPexoQualExample | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, Genome |
| Version | 1.36.0 |
| License | GPL (>= 2) |
| Depends | R (>= 3.3) |
| Imports | |
| System Requirements | |
| URL | http://www.github.com/keleslab/ChIPexoQualExample |
See More
| Suggests | BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | ChIPexoQual |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ChIPexoQualExample_1.36.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/ChIPexoQualExample |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ChIPexoQualExample |
| Package Short Url | https://bioconductor.org/packages/ChIPexoQualExample/ |
| Package Downloads Report | Download Stats |