recipe bioconductor-netzoor

Unified methods for the inference and analysis of gene regulatory networks

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-netzoor/meta.yaml

netZooR unifies the implementations of several Network Zoo methods (netzoo, netzoo.github.io) into a single package by creating interfaces between network inference and network analysis methods. Currently, the package has 3 methods for network inference including PANDA and its optimized implementation OTTER (network reconstruction using mutliple lines of biological evidence), LIONESS (single-sample network inference), and EGRET (genotype-specific networks). Network analysis methods include CONDOR (community detection), ALPACA (differential community detection), CRANE (significance estimation of differential modules), MONSTER (estimation of network transition states). In addition, YARN allows to process gene expresssion data for tissue-specific analyses and SAMBAR infers missing mutation data based on pathway information.

package bioconductor-netzoor

versions:

1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-go.db:

>=3.18.0,<3.19.0

depends bioconductor-gostats:

>=2.68.0,<2.69.0

depends bioconductor-org.hs.eg.db:

>=3.18.0,<3.19.0

depends bioconductor-pandar:

>=1.34.0,<1.35.0

depends bioconductor-rcy3:

>=2.22.0,<2.23.0

depends bioconductor-stringdb:

>=2.14.0,<2.15.0

depends bioconductor-yarn:

>=1.28.0,<1.29.0

depends r-assertthat:

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-doparallel:

depends r-dplyr:

depends r-foreach:

depends r-ggdendro:

depends r-ggplot2:

depends r-gplots:

depends r-igraph:

depends r-mass:

depends r-matrix:

depends r-matrixcalc:

depends r-matrixstats:

depends r-nnet:

depends r-penalized:

depends r-reshape:

depends r-reshape2:

depends r-reticulate:

depends r-tidyr:

depends r-vegan:

depends r-viridislite:

requirements:

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-netzoor

and update with::

   mamba update bioconductor-netzoor

To create a new environment, run:

mamba create --name myenvname bioconductor-netzoor

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-netzoor:<tag>

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

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