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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ClassifyR")
In most cases, you don't need to download the package archive at all.
ClassifyR
A framework for two-class classification problems, with applications to differential variability and differential distribution testing.
Bioconductor version: 3.0
The software formalises a framework for classification in R. There are four stages. Data transformation, feature selection, 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 does a couple of cross-validation schemes. Functions for differential expression, differential variability, and differential distribution are included. Additional functions may be developed by the user, if they have better performing methods.
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:
source("http://bioconductor.org/biocLite.R")
biocLite("ClassifyR")
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 |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Classification, Software, Survival |
| Version | 1.0.18 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | GPL-3 |
| Depends | R (>= 3.0.3), methods, Biobase, BiocParallel |
| Imports | locfit, ROCR, grid |
| LinkingTo | |
| Suggests | limma, edgeR, car, Rmixmod, ggplot2, gridExtra, BiocStyle, pamr, sparsediscrim, PoiClaClu, curatedOvarianData, parathyroidSE, knitr, klaR, gtable, scales |
| 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.
| Package Source | ClassifyR_1.0.18.tar.gz |
| Windows Binary | ClassifyR_1.0.18.zip |
| Mac OS X 10.6 (Snow Leopard) | ClassifyR_1.0.18.tgz |
| Mac OS X 10.9 (Mavericks) | ClassifyR_1.0.18.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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