IntOMICS

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

This package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see .

Integrative analysis of multi-omics data to infer regulatory networks

Bioconductor version: Development (3.19)

IntOMICSr is an efficient integrative framework based on Bayesian networks. IntOMICSr systematically analyses gene expression (GE), DNA methylation (METH), copy number variation (CNV) and biological prior knowledge (B) to infer regulatory networks. IntOMICSr complements the missing biological prior knowledge by so-called empirical biological knowledge (empB), estimated from the available experimental data. An automatically tuned MCMC algorithm (Yang and Rosenthal, 2017) estimates model parameters and the empirical biological knowledge. Conventional MCMC algorithm with additional Markov blanket resampling (MBR) step (Su and Borsuk, 2016) infers resulting regulatory network structure consisting of three types of nodes: GE nodes refer to gene expression levels, CNV nodes refer to associated copy number variations, and METH nodes refer to associated DNA methylation probe(s).

Author: Pacinkova Anna [cre, aut]

Maintainer: Pacinkova Anna <ana.pacinkova at gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


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

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

BiocManager::install("IntOMICS")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bayesian, CopyNumberVariation, DNAMethylation, GeneExpression, GeneRegulation, Network, Software, SystemsBiology
Version	1.3.1
In Bioconductor since	BioC 3.17 (R-4.3) (1 year)
License	GPL-3
Depends
Imports	bnlearn, bnstruct, matrixStats, RColorBrewer, bestNormalize, igraph, gplots, stats, utils, graphics, numbers, SummarizedExperiment, ggplot2, ggraph, methods, cowplot, grid, rlang
System Requirements
URL	https://github.com/anna-pacinkova/IntOMICSr
Bug Reports	https://github.com/anna-pacinkova/IntOMICSr/issues

Suggests	BiocStyle, knitr, rmarkdown, curatedTCGAData, TCGAutils, testthat
Linking To
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Build Report	Build Report

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/IntOMICS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/IntOMICS
Package Short Url	https://bioconductor.org/packages/IntOMICS/
Package Downloads Report	Download Stats