SigCheck

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

Bioconductor version: Release (3.20)

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 (version "4.4") and enter:


if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, GeneExpression, GeneSetEnrichment, Software
Version	2.38.0
In Bioconductor since	BioC 3.0 (R-3.1) (10 years)
License	Artistic-2.0
Depends	R (>= 4.0.0), MLInterfaces, Biobase, e1071, BiocParallel, survival
Imports	graphics, stats, utils, methods
System Requirements
URL

Suggests	BiocStyle, breastCancerNKI, qusage
Linking To
Enhances
Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package	SigCheck_2.38.0.tar.gz
Windows Binary (x86_64)	SigCheck_2.38.0.zip
macOS Binary (x86_64)	SigCheck_2.38.0.tgz
macOS Binary (arm64)	SigCheck_2.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SigCheck
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SigCheck
Bioc Package Browser	https://code.bioconductor.org/browse/SigCheck/
Package Short Url	https://bioconductor.org/packages/SigCheck/
Package Downloads Report	Download Stats