ClassifyR

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ClassifyR.

A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing


Bioconductor version: 3.14

The software formalises a framework for classification in R. There are four stages; Data transformation, feature selection, classifier training, and prediction. The requirements of variable types and names are fixed, but specialised variables for functions can also be provided. The classification framework is wrapped in a driver loop, that reproducibly carries out a number of cross-validation schemes. Functions for differential expression, differential variability, and differential distribution are included. Additional functions may be developed by the user, by creating an interface to the framework.

Author: Dario Strbenac, John Ormerod, Graham Mann, Jean Yang

Maintainer: Dario Strbenac <dario.strbenac at sydney.edu.au>

Citation (from within R, enter citation("ClassifyR")):

Installation

To install this package, start R (version "4.1") and enter:


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

BiocManager::install("ClassifyR")

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("ClassifyR")
An Introduction to the ClassifyR Package HTML R Script
Example: Creating a Wrapper Function for the k-NN Classifier HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Software, Survival
Version 2.14.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL-3
Depends R (>= 3.5.0), methods, S4Vectors(>= 0.18.0), MultiAssayExperiment(>= 1.6.0), BiocParallel
Imports locfit, grid, utils, plyr, MultiAssayExperiment(>= 1.6.0)
System Requirements
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Suggests limma, genefilter, edgeR, car, Rmixmod, ggplot2 (>= 3.0.0), gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, parathyroidSE, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, randomForest, robustbase, glmnet, class
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Package Archives

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

Source Package ClassifyR_2.14.0.tar.gz
Windows Binary ClassifyR_2.14.0.zip
macOS 10.13 (High Sierra) ClassifyR_2.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ClassifyR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ClassifyR
Bioc Package Browser https://code.bioconductor.org/browse/ClassifyR/
Package Short Url https://bioconductor.org/packages/ClassifyR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive