BioMM

DOI: 10.18129/B9.bioc.BioMM    

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

Bioconductor version: Release (3.9)

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 various prior biological meta information.

Author: Junfang Chen and Emanuel Schwarz

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

Citation (from within R, enter citation("BioMM")):

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("BioMM")

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("BioMM")

 

HTML R Script BioMMtutorial
PDF   Reference Manual
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Details

biocViews Classification, GO, Genetics, Pathways, Regression, Software
Version 1.0.0
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
License GPL-3
Depends R (>= 3.6)
Imports stats, utils, grDevices, lattice, BiocParallel, glmnet, rms, nsprcomp, ranger, e1071, variancePartition, ggplot2
LinkingTo
Suggests BiocStyle, knitr, RUnit, BiocGenerics
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report  

Package Archives

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

Source Package BioMM_1.0.0.tar.gz
Windows Binary BioMM_1.0.0.zip
Mac OS X 10.11 (El Capitan) BioMM_1.0.0.tgz
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

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