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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 (3.19)

The software formalises a framework for classification and survival model evaluation in R. There are four stages; Data transformation, feature selection, model training, and prediction. The requirements of variable types and variable order are fixed, but specialised variables for functions can also be provided. The framework is wrapped in a driver loop that reproducibly carries out a number of cross-validation schemes. Functions for differential mean, 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 [aut, cre], Ellis Patrick [aut], Sourish Iyengar [aut], Harry Robertson [aut], Andy Tran [aut], John Ormerod [aut], Graham Mann [aut], Jean Yang [aut]

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

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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
Developer's Guide HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Software, Survival
Version 3.7.3
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL-3
Depends R (>= 4.1.0), generics, methods, S4Vectors, MultiAssayExperiment, BiocParallel, survival
Imports grid, genefilter, utils, dplyr, tidyr, rlang, ranger, ggplot2 (>= 3.0.0), ggpubr, reshape2, ggupset
System Requirements
URL https://sydneybiox.github.io/ClassifyR/
See More
Suggests limma, edgeR, car, Rmixmod, gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, parathyroidSE, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, robustbase, glmnet, class, randomForestSRC, MatrixModels, xgboost, data.tree, ggnewscale
Linking To
Enhances
Depends On Me
Imports Me spicyR, TOP
Suggests Me scFeatures, spicyWorkflow, Statial
Links To Me
Build Report Build Report

Package Archives

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

Source Package ClassifyR_3.7.3.tar.gz
Windows Binary ClassifyR_3.7.3.zip (64-bit only)
macOS Binary (x86_64) ClassifyR_3.7.2.tgz
macOS Binary (arm64) ClassifyR_3.7.3.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