SigCheck
This package is for version 3.10 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: 3.10
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("SigCheck")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, GeneExpression, GeneSetEnrichment, Software |
| Version | 2.18.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.2.0), MLInterfaces, Biobase, e1071, BiocParallel, survival |
| Imports | graphics, stats, utils, methods |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, breastCancerNKI, qusage |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SigCheck_2.18.0.tar.gz |
| Windows Binary | SigCheck_2.18.0.zip |
| Mac OS X 10.11 (El Capitan) | SigCheck_2.18.0.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 |
| Old Source Packages for BioC 3.10 | Source Archive |