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To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("CancerMutationAnalysis")
In most cases, you don't need to download the package archive at all.
CancerMutationAnalysis
Cancer mutation analysis
Bioconductor version: 3.1
This package implements gene and gene-set level analysis methods for somatic mutation studies of cancer. The gene-level methods distinguish between driver genes (which play an active role in tumorigenesis) and passenger genes (which are mutated in tumor samples, but have no role in tumorigenesis) and incorporate a two-stage study design. The gene-set methods implement a patient-oriented approach, which calculates gene-set scores for each sample, then combines them across samples; a gene-oriented approach which uses the Wilcoxon test is also provided for comparison.
Author: Giovanni Parmigiani, Simina M. Boca
Maintainer: Simina M. Boca <simina.boca at nih.gov>
Citation (from within R,
enter citation("CancerMutationAnalysis")):
Installation
To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("CancerMutationAnalysis")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CancerMutationAnalysis")
| CancerMutationAnalysisTutorial | ||
| Reference Manual | ||
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | Genetics, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (3.5 years) |
| License | GPL (>= 2) + file LICENSE |
| Depends | R (>= 2.10.0), qvalue |
| Imports | AnnotationDbi, limma, methods, stats |
| LinkingTo | |
| Suggests | KEGG.db |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | CancerMutationAnalysis_1.12.0.tar.gz |
| Windows Binary | CancerMutationAnalysis_1.12.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | CancerMutationAnalysis_1.12.0.tgz |
| Mac OS X 10.9 (Mavericks) | CancerMutationAnalysis_1.12.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/CancerMutationAnalysis/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/CancerMutationAnalysis/ |
| Package Downloads Report | Download Stats |
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