SigCheck

DOI: 10.18129/B9.bioc.SigCheck    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see SigCheck.

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

Bioconductor version: 3.11

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SigCheck")

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("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	2.20.0
In Bioconductor since	BioC 3.0 (R-3.1) (6 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
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SigCheck_2.20.0.tar.gz
Windows Binary	SigCheck_2.20.0.zip
macOS 10.13 (High Sierra)	SigCheck_2.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SigCheck
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SigCheck
Package Short Url	https://bioconductor.org/packages/SigCheck/
Package Downloads Report	Download Stats