SigCheck
This is thereleased version of SigCheck; for the devel version, seeSigCheck.
Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata
Bioconductor version: Release (3.22)
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("SigCheck")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("SigCheck")For older versions of R, please refer to the appropriateBioconductor 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 | 2.42.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (11 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0.0),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 | |
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| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | SigCheck_2.42.0.tar.gz |
| Windows Binary (x86_64) | SigCheck_2.42.0.zip |
| macOS Binary (x86_64) | SigCheck_2.42.0.tgz |
| macOS Binary (arm64) | SigCheck_2.42.0.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 |