CNTools
This is the development version of CNTools; for the stable release version, see CNTools.
Convert segment data into a region by sample matrix to allow for other high level computational analyses.
Bioconductor version: Development (3.24)
This package provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data
Author: Jianhua Zhang
Maintainer: J. Zhang <jzhang at jimmy.harvard.edu>
citation("CNTools")):
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("CNTools")
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("CNTools")| NCTools HowTo | R Script | |
| Reference Manual |
Details
| biocViews | CopyNumberVariation, Microarray, Software |
| Version | 1.69.0 |
| In Bioconductor since | BioC 2.5 (R-2.10) (17 years) |
| License | LGPL |
| Depends | R (>= 2.10), methods, tools, stats, genefilter |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | cghMCR |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CNTools_1.69.0.tar.gz |
| Windows Binary (x86_64) | CNTools_1.69.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | CNTools_1.69.0.tgz |
| macOS Binary (sonoma-arm64) | CNTools_1.69.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CNTools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CNTools |
| Bioc Package Browser | https://code.bioconductor.org/browse/CNTools/ |
| Package Short Url | https://bioconductor.org/packages/CNTools/ |
| Package Downloads Report | Download Stats |