CancerMutationAnalysis
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CancerMutationAnalysis.
Cancer mutation analysis
Bioconductor version: 3.9
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 <smb310 at georgetown.edu>
citation("CancerMutationAnalysis")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CancerMutationAnalysis")
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("CancerMutationAnalysis")| CancerMutationAnalysisTutorial | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Genetics, Software |
| Version | 1.26.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (12 years) |
| License | GPL (>= 2) + file LICENSE |
| Depends | R (>= 2.10.0), qvalue |
| Imports | AnnotationDbi, limma, methods, stats |
| System Requirements | |
| URL |
See More
| Suggests | KEGG.db |
| Linking To | |
| Enhances | |
| Depends On Me | |
| 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 | CancerMutationAnalysis_1.26.0.tar.gz |
| Windows Binary | CancerMutationAnalysis_1.26.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | CancerMutationAnalysis_1.26.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CancerMutationAnalysis |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CancerMutationAnalysis |
| Bioc Package Browser | https://code.bioconductor.org/browse/CancerMutationAnalysis/ |
| Package Short Url | https://bioconductor.org/packages/CancerMutationAnalysis/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |