ClassifyR

DOI: 10.18129/B9.bioc.ClassifyR  

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

Bioconductor version: Release (3.17)

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>

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	An Introduction to the ClassifyR Package
HTML	R Script	Developer's Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, Software, Survival
Version	3.4.11
In Bioconductor since	BioC 3.0 (R-3.1) (9 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
LinkingTo
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
SystemRequirements
Enhances
URL	https://sydneybiox.github.io/ClassifyR/
Depends On Me
Imports Me	spicyR, TOP
Suggests Me	scFeatures, spicyWorkflow, Statial
Links To Me
Build Report

Package Archives

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

Source Package	ClassifyR_3.4.11.tar.gz
Windows Binary	ClassifyR_3.4.11.zip (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64)	ClassifyR_3.4.11.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 3.17	Source Archive