ClassifyR

DOI: 10.18129/B9.bioc.ClassifyR    

This is the development version of ClassifyR; for the stable release version, see ClassifyR.

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

Bioconductor version: Development (3.8)

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 and enter:

if (!require("BiocManager"))
    install.packages("BiocManager")
BiocManager::install("ClassifyR", version = "devel")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ClassifyR")

 

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

Details

biocViews Classification, Software, Survival
Version 2.1.10
In Bioconductor since BioC 3.0 (R-3.1) (4 years)
License GPL-3
Depends R (>= 3.5.0), methods, S4Vectors(>= 0.18.0), MultiAssayExperiment(>= 1.6.0), BiocParallel
Imports locfit, grid, utils, plyr
LinkingTo
Suggests limma, genefilter, edgeR, car, Rmixmod, ggplot2 (>= 2.2.0), gridExtra (>= 2.0.0), BiocStyle, pamr, sparsediscrim, PoiClaClu, parathyroidSE, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, randomForest, robustbase, mlogit, mnlogit, glmnet, class
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package ClassifyR_2.1.10.tar.gz
Windows Binary ClassifyR_2.1.10.zip
Mac OS X 10.11 (El Capitan) ClassifyR_2.1.10.tgz
Source Repository git clone https://git.bioconductor.org/packages/ClassifyR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ClassifyR
Package Short Url http://bioconductor.org/packages/ClassifyR/
Package Downloads Report Download Stats

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