recipe bioconductor-omnipathr

OmniPath web service client and more

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-omnipathr/meta.yaml

A client for the OmniPath web service (https://www.omnipathdb.org) and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github).

package bioconductor-omnipathr

versions:

3.10.1-0,  3.8.0-0,  3.5.25-0,  3.2.0-0,  3.0.0-0,  2.0.0-1,  2.0.0-0,  1.2.0-0,  1.0.0-0

depends r-base:

>=4.3,<4.4.0a0

depends r-checkmate:

depends r-crayon:

depends r-curl:

depends r-digest:

depends r-dplyr:

>=1.1.0

depends r-httr:

depends r-igraph:

depends r-jsonlite:

depends r-later:

depends r-logger:

depends r-lubridate:

depends r-magrittr:

depends r-progress:

depends r-purrr:

depends r-rappdirs:

depends r-readr:

>=2.0.0

depends r-readxl:

depends r-rlang:

depends r-rmarkdown:

depends r-rvest:

depends r-stringi:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

depends r-tidyselect:

depends r-withr:

depends r-xml2:

depends r-yaml:

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-omnipathr

and update with::

   mamba update bioconductor-omnipathr

To create a new environment, run:

mamba create --name myenvname bioconductor-omnipathr

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-omnipathr:<tag>

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

Download stats

Link to this page

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