recipe bioconductor-ontoproc

processing of ontologies of anatomy, cell lines, and so on

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-ontoproc/meta.yaml

Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN. We provide snapshots of key ontologies for terms about cells, cell lines, chemical compounds, and anatomy, to help analyze genome-scale experiments, particularly cell x compound screens. Another purpose is to strengthen development of compelling use cases for richer interfaces to emerging ontologies.

package bioconductor-ontoproc

versions:

1.24.0-0,  1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0, 

1.24.0-0,  1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.4.0-0

depends bioconductor-annotationhub:

>=3.10.0,<3.11.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocfilecache:

>=2.10.0,<2.11.0

depends bioconductor-graph:

>=1.80.0,<1.81.0

depends bioconductor-rgraphviz:

>=2.46.0,<2.47.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-dt:

depends r-igraph:

depends r-magrittr:

depends r-ontologyindex:

depends r-ontologyplot:

depends r-shiny:

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-ontoproc

and update with::

   mamba update bioconductor-ontoproc

To create a new environment, run:

mamba create --name myenvname bioconductor-ontoproc

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-ontoproc:<tag>

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

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