recipe bioconductor-kegglincs

Visualize all edges within a KEGG pathway and overlay LINCS data

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/KEGGlincs.html

License:

GPL-3

Recipe:

/bioconductor-kegglincs/meta.yaml

Links:

biotools: kegglincs, doi: 10.7490/f1000research.1113436.1

See what is going on 'under the hood' of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.

package bioconductor-kegglincs

versions:

1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0, 

1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.10.0-1,  1.8.0-0,  1.6.2-0,  1.4.0-0

depends bioconductor-annotationdbi:

>=1.68.0,<1.69.0

depends bioconductor-hgu133a.db:

>=3.13.0,<3.14.0

depends bioconductor-kegggraph:

>=1.66.0,<1.67.0

depends bioconductor-keggrest:

>=1.46.0,<1.47.0

depends bioconductor-kodata:

>=1.32.0,<1.33.0

depends bioconductor-org.hs.eg.db:

>=3.20.0,<3.21.0

depends cytoscape:

>=3.3.0

depends r-base:

>=4.4,<4.5.0a0

depends r-gtools:

depends r-httr:

depends r-igraph:

depends r-plyr:

depends r-rjsonio:

depends r-xml:

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-kegglincs

and update with::

   mamba update bioconductor-kegglincs

To create a new environment, run:

mamba create --name myenvname bioconductor-kegglincs

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-kegglincs:<tag>

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

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