CoverageView
This is the development version of CoverageView; for the stable release version, see CoverageView.
Coverage visualization package for R
Bioconductor version: Development (3.24)
This package provides a framework for the visualization of genome coverage profiles. It can be used for ChIP-seq experiments, but it can be also used for genome-wide nucleosome positioning experiments or other experiment types where it is important to have a framework in order to inspect how the coverage distributed across the genome
Author: Ernesto Lowy
Maintainer: Ernesto Lowy <ernestolowy at gmail.com>
citation("CoverageView")):
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("CoverageView")
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("CoverageView")| Easy visualization of the read coverage | R Script | |
| Reference Manual |
Details
| biocViews | ChIPSeq, ImmunoOncology, RNASeq, Sequencing, Software, Technology, Visualization |
| Version | 1.51.1 |
| In Bioconductor since | BioC 2.14 (R-3.1) (12.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), methods, Rsamtools(>= 1.19.17), rtracklayer |
| Imports | S4Vectors(>= 0.7.21), IRanges(>= 2.3.23), GenomicRanges, GenomicAlignments, parallel, tools |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CoverageView_1.51.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | CoverageView_1.51.1.tgz |
| macOS Binary (sonoma-arm64) | CoverageView_1.51.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CoverageView |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CoverageView |
| Bioc Package Browser | https://code.bioconductor.org/browse/CoverageView/ |
| Package Short Url | https://bioconductor.org/packages/CoverageView/ |
| Package Downloads Report | Download Stats |