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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GeneSelector")
In most cases, you don't need to download the package archive at all.
GeneSelector
Stability and Aggregation of ranked gene lists
Bioconductor version: 3.0
The term 'GeneSelector' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list in various ranking methods (currently 14). In addition, the stability of the findings can be taken into account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise. Given multiple ranked lists, one can use aggregation methods in order to find a synthesis.
Author: Martin Slawski <ms at cs.uni-sb.de>, Anne-Laure Boulesteix <boulesteix at ibe.med.uni-muenchen.de>.
Maintainer: Martin Slawski <ms at cs.uni-sb.de>
Citation (from within R,
enter citation("GeneSelector")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GeneSelector")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GeneSelector")
| R Script | GeneSelector.pdf | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, Software, StatisticalMethod |
| Version | 2.16.0 |
| In Bioconductor since | BioC 2.2 (R-2.7) |
| License | GPL (>= 2) |
| Depends | R (>= 2.5.1), methods, stats, Biobase |
| Imports | multtest, siggenes, samr, limma |
| LinkingTo | |
| Suggests | multtest, siggenes, samr, limma |
| 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 | GeneSelector_2.16.0.tar.gz |
| Windows Binary | GeneSelector_2.16.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | GeneSelector_2.16.0.tgz |
| Mac OS X 10.9 (Mavericks) | GeneSelector_2.16.0.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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