recipe bioconductor-intomics

Integrative analysis of multi-omics data to infer regulatory networks

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/IntOMICS.html

License:

GPL-3

Recipe:

/bioconductor-intomics/meta.yaml

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).

package bioconductor-intomics

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-bestnormalize:

depends r-bnlearn:

depends r-bnstruct:

depends r-cowplot:

depends r-ggplot2:

depends r-ggraph:

depends r-gplots:

depends r-igraph:

depends r-matrixstats:

depends r-numbers:

depends r-rcolorbrewer:

depends r-rlang:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-intomics

and update with::

   mamba update bioconductor-intomics

To create a new environment, run:

mamba create --name myenvname bioconductor-intomics

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-intomics:<tag>

(see `bioconductor-intomics/tags`_ for valid values for ``<tag>``)

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