ClassifyR
A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing
Bioconductor version: Release (3.20)
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("ClassifyR")):
Installation
To install this package, start R (version "4.4") 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 |
| Developer's Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Software, Survival |
| Version | 3.10.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (10 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 | TOP, spicyR |
| Suggests Me | Statial, scFeatures, spicyWorkflow |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ClassifyR_3.10.0.tar.gz |
| Windows Binary (x86_64) | ClassifyR_3.10.0.zip (64-bit only) |
| macOS Binary (x86_64) | ClassifyR_3.10.0.tgz |
| macOS Binary (arm64) | ClassifyR_3.9.5.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 |