This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see SigCheck.
Bioconductor version: 3.17
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 <bioconductor at starkhome.com> and Justin Norden
Maintainer: Rory Stark <bioconductor at starkhome.com>
Citation (from within R,
enter citation("SigCheck")
):
To install this package, start R (version "4.3") 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.
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 |
biocViews | Classification, GeneExpression, GeneSetEnrichment, Software |
Version | 2.32.1 |
In Bioconductor since | BioC 3.0 (R-3.1) (9 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 |
Follow Installation instructions to use this package in your R session.
Source Package | SigCheck_2.32.1.tar.gz |
Windows Binary | SigCheck_2.32.1.zip |
macOS Binary (x86_64) | SigCheck_2.32.1.tgz |
macOS Binary (arm64) | SigCheck_2.32.1.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/SigCheck |
Source Repository (Developer Access) | git clone [email protected]:packages/SigCheck |
Bioc Package Browser | https://code.bioconductor.org/browse/SigCheck/ |
Package Short Url | https://bioconductor.org/packages/SigCheck/ |
Package Downloads Report | Download Stats |
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