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: 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("IntOMICS")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("IntOMICS")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Bayesian, CopyNumberVariation, DNAMethylation, GeneExpression, GeneRegulation, Network, Software, SystemsBiology |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
| 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 |
See More
| Suggests | BiocStyle, knitr, rmarkdown, curatedTCGAData, TCGAutils, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| 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 |