To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SigCheck")

In most cases, you don't need to download the package archive at all.

SigCheck

DOI: 10.18129/B9.bioc.SigCheck    

This is the development version of SigCheck; for the stable release version, see SigCheck.

Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata

Bioconductor version: Development (3.6)

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

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:// URLs are not supported
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")

 

PDF R Script Checking gene expression signatures against random and known signatures with SigCheck
PDF   Reference Manual
Text   NEWS

Details

biocViews Classification, GeneExpression, GeneSetEnrichment, Software
Version 2.9.0
In Bioconductor since BioC 3.0 (R-3.1) (3 years)
License Artistic-2.0
Depends R (>= 3.2.0), MLInterfaces, Biobase, e1071, BiocParallel, survival
Imports graphics, stats, utils, methods
LinkingTo
Suggests BiocStyle, breastCancerNKI, qusage
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.

Source Package SigCheck_2.9.0.tar.gz
Windows Binary SigCheck_2.9.0.zip
Mac OS X 10.11 (El Capitan) SigCheck_2.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SigCheck
Package Short Url http://bioconductor.org/packages/SigCheck/
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