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BioMM

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

Bioconductor version: Release (3.17)

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>

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

Installation

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

if (!require("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")
BioMMtutorial HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, GO, Genetics, Pathways, Regression, Software
Version 1.15.0
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
Linking To
Suggests BiocStyle, knitr, RUnit, BiocGenerics
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Package Archives

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

Source Package BioMM_1.15.0.tar.gz
Windows Binary BioMM_1.15.0.zip
macOS Binary (x86_64)
macOS Binary (arm64) BioMM_1.15.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BioMM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BioMM
Bioc Package Browser https://code.bioconductor.org/browse/BioMM/
Package Short Url https://bioconductor.org/packages/BioMM/
Package Downloads Report Download Stats