BioMM

DOI: 10.18129/B9.bioc.BioMM  

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of BioMM; for the stable release version, see BioMM.

BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data

Bioconductor version: Development (3.18)

The identification of reproducible biological patterns from high-dimensional omics data is a key factor in understanding the biology of complex disease or traits. Incorporating prior biological knowledge into machine learning is an important step in advancing such research. We have proposed a biologically informed multi-stage machine learing framework termed BioMM specifically for phenotype prediction based on omics-scale data where we can evaluate different machine learning models with prior biological meta information.

Author: Junfang Chen and Emanuel Schwarz

Maintainer: Junfang Chen <junfang.chen33 at gmail.com>

Installation

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

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

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

BiocManager::install("BioMM")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	Classification, GO, Genetics, Pathways, Regression, Software
Version	1.17.1
In Bioconductor since	BioC 3.9 (R-3.6) (4.5 years)
License	GPL-3
Depends	R (>= 3.6)
Imports	stats, utils, grDevices, lattice, BiocParallel, glmnet, rms, precrec, nsprcomp, ranger, e1071, ggplot2, vioplot, CMplot, imager, topGO, xlsx
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Suggests	BiocStyle, knitr, RUnit, BiocGenerics
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/BioMM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BioMM
Package Short Url	https://bioconductor.org/packages/BioMM/
Package Downloads Report	Download Stats