CGHnormaliter
This is the released version of CGHnormaliter; for the devel version, see CGHnormaliter.
Normalization of array CGH data with imbalanced aberrations.
Bioconductor version: Release (3.23)
Normalization and centralization of array comparative genomic hybridization (aCGH) data. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs).
Author: Bart P.P. van Houte, Thomas W. Binsl, Hannes Hettling
Maintainer: Bart P.P. van Houte <bvhoute at few.vu.nl>
citation("CGHnormaliter")):
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("CGHnormaliter")
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("CGHnormaliter")| CGHnormaliter | R Script | |
| Reference Manual |
Details
| biocViews | Microarray, Preprocessing, Software |
| Version | 1.66.0 |
| In Bioconductor since | BioC 2.5 (R-2.10) (17 years) |
| License | GPL (>= 3) |
| Depends | CGHcall(>= 2.17.0), CGHbase(>= 1.15.0) |
| Imports | Biobase, CGHbase, CGHcall, methods, stats, utils |
| System Requirements | |
| URL |
See More
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CGHnormaliter_1.66.0.tar.gz |
| Windows Binary (x86_64) | CGHnormaliter_1.66.0.zip |
| macOS Binary (big-sur-x86_64) | CGHnormaliter_1.66.0.tgz |
| macOS Binary (sonoma-arm64) | CGHnormaliter_1.66.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CGHnormaliter |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CGHnormaliter |
| Bioc Package Browser | https://code.bioconductor.org/browse/CGHnormaliter/ |
| Package Short Url | https://bioconductor.org/packages/CGHnormaliter/ |
| Package Downloads Report | Download Stats |