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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("SigCheck")
In most cases, you don't need to download the package archive at all.
SigCheck
Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata
Bioconductor version: 3.1
While gene signatures are frequently used to predict phenotypes (e.g. predict prognosis of cancer patients), it it not always clear how optimal or meaningful they are (cf David Venet, Jacques E. Dumont, and Vincent Detours' paper "Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome"). Based on suggestions in that paper, SigCheck accepts a data set (as an ExpressionSet) and a gene signature, and compares its performance on survival and/or classification tasks against a) random gene signatures of the same length; b) known, related and unrelated gene signatures; and c) permuted data and/or metadata.
Author: Rory Stark <rory.stark at cruk.cam.ac.uk> and Justin Norden <jn333 at cam.ac.uk>
Maintainer: Rory Stark <rory.stark at cruk.cam.ac.uk>
Citation (from within R,
enter citation("SigCheck")):
Installation
To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("SigCheck")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SigCheck")
| R Script | Checking gene expression signatures against random and known signatures with SigCheck | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Classification, GeneExpression, GeneSetEnrichment, Software |
| Version | 2.0.2 |
| In Bioconductor since | BioC 3.0 (R-3.1) (1 year) |
| License | Artistic-2.0 |
| Depends | R (>= 3.1.0), MLInterfaces, Biobase, e1071, BiocParallel, survival |
| Imports | graphics, stats, utils, methods |
| LinkingTo | |
| Suggests | BiocStyle, breastCancerNKI |
| 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 | SigCheck_2.0.2.tar.gz |
| Windows Binary | SigCheck_2.0.2.zip |
| Mac OS X 10.6 (Snow Leopard) | SigCheck_2.0.2.tgz |
| Mac OS X 10.9 (Mavericks) | SigCheck_2.0.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/SigCheck/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/SigCheck/ |
| Package Downloads Report | Download Stats |
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