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To install this package, start R and enter:
source("http://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: 3.0
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:
source("http://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 | 1.10.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) |
| 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_1.10.0.tar.gz |
| Windows Binary | CancerMutationAnalysis_1.10.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | CancerMutationAnalysis_1.10.0.tgz |
| Mac OS X 10.9 (Mavericks) | CancerMutationAnalysis_1.10.0.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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