recipe bioconductor-genenetworkbuilder

GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data

Homepage:

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

License:

GPL-3.0-or-later

Recipe:

/bioconductor-genenetworkbuilder/meta.yaml

Links:

biotools: genenetworkbuilder

Appliation for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, GeneNetworkBuilder generates a regulatory network of the TF.

package bioconductor-genenetworkbuilder

versions:

1.48.0-0,  1.44.0-1,  1.44.0-0,  1.42.0-0,  1.40.0-1,  1.40.0-0,  1.36.1-1,  1.36.1-0,  1.36.0-0, 

1.48.0-0,  1.44.0-1,  1.44.0-0,  1.42.0-0,  1.40.0-1,  1.40.0-0,  1.36.1-1,  1.36.1-0,  1.36.0-0,  1.34.0-0,  1.32.0-1,  1.32.0-0,  1.30.0-0,  1.28.0-0,  1.26.1-0,  1.24.1-0,  1.24.0-0

depends bioconductor-graph:

>=1.84.0,<1.85.0

depends bioconductor-graph:

>=1.84.0,<1.85.0a0

depends bioconductor-rcy3:

>=2.26.0,<2.27.0

depends bioconductor-rcy3:

>=2.26.0,<2.27.0a0

depends bioconductor-rgraphviz:

>=2.50.0,<2.51.0

depends bioconductor-rgraphviz:

>=2.50.0,<2.51.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

depends r-htmlwidgets:

depends r-plyr:

depends r-rcpp:

>=0.9.13

depends r-rjson:

depends r-xml:

requirements:

additional platforms:

linux-aarch64

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-genenetworkbuilder

and update with::

   mamba update bioconductor-genenetworkbuilder

To create a new environment, run:

mamba create --name myenvname bioconductor-genenetworkbuilder

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-genenetworkbuilder:<tag>

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

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