ClassifyR
This package is for version 3.11 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: 3.11
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("ClassifyR")):
Installation
To install this package, start R (version "4.0") 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 | ||
| NEWS | Text |
Details
| biocViews | Classification, Software, Survival |
| Version | 2.8.0 |
| 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 |
| System Requirements | |
| URL |
See More
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ClassifyR_2.8.0.tar.gz |
| Windows Binary | ClassifyR_2.8.0.zip |
| macOS 10.13 (High Sierra) | ClassifyR_2.8.0.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 3.11 | Source Archive |