IntOMICS
Integrative analysis of multi-omics data to infer regulatory networks
Bioconductor version: Release (3.17)
IntOMICS is an efficient integrative framework based on Bayesian networks. IntOMICS systematically analyses gene expression (GE), DNA methylation (METH), copy number variation (CNV) and biological prior knowledge (B) to infer regulatory networks. IntOMICS 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 "4.3") 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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("IntOMICS")| IntOMICS tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, CopyNumberVariation, DNAMethylation, GeneExpression, GeneRegulation, Network, Software, SystemsBiology |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (< 6 months) |
| License | GPL-3 |
| Depends | |
| Imports | bnlearn, bnstruct, matrixStats, RColorBrewer, bestNormalize, igraph, gplots, stats, utils, graphics, numbers, SummarizedExperiment, ggplot2, ggraph, methods, cowplot, grid, rlang |
| Linking To | |
| Suggests | BiocStyle, knitr, rmarkdown, curatedTCGAData, TCGAutils, testthat |
| System Requirements | |
| Enhances | |
| URL | https://github.com/anna-pacinkova/IntOMICS |
| Bug Reports | https://github.com/anna-pacinkova/IntOMICS/issues |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | IntOMICS_1.0.0.tar.gz |
| Windows Binary | IntOMICS_1.0.0.zip |
| macOS Binary (x86_64) | IntOMICS_1.0.0.tgz |
| macOS Binary (arm64) | IntOMICS_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/IntOMICS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/IntOMICS |
| Bioc Package Browser | https://code.bioconductor.org/browse/IntOMICS/ |
| Package Short Url | https://bioconductor.org/packages/IntOMICS/ |
| Package Downloads Report | Download Stats |