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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("CNAnorm")
In most cases, you don't need to download the package archive at all.
CNAnorm
A normalization method for Copy Number Aberration in cancer samples
Bioconductor version: 3.0
Performs ratio, GC content correction and normalization of data obtained using low coverage (one read every 100-10,000 bp) high troughput sequencing. It performs a "discrete" normalization looking for the ploidy of the genome. It will also provide tumour content if at least two ploidy states can be found.
Author: Stefano Berri <sberri at illumina.com>, Henry M. Wood <H.M.Wood at leeds.ac.uk>, Arief Gusnanto <a.gusnanto at leeds.ac.uk>
Maintainer: Stefano Berri <sberri at illumina.com>
Citation (from within R,
enter citation("CNAnorm")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("CNAnorm")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CNAnorm")
| CNAnorm.pdf | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumberVariation, Coverage, DNASeq, GenomicVariation, Normalization, Sequencing, Software, WholeGenome |
| Version | 1.12.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | GPL-2 |
| Depends | R (>= 2.10.1), methods |
| Imports | DNAcopy |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | http://www.r-project.org |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | CNAnorm_1.12.0.tar.gz |
| Windows Binary | CNAnorm_1.12.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | CNAnorm_1.12.0.tgz |
| Mac OS X 10.9 (Mavericks) | CNAnorm_1.12.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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