recipe bioconductor-omnipathr

OmniPath web service client and more

Homepage:

https://bioconductor.org/packages/3.16/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:

3.5.25-0,  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 >=4.2,<4.3.0a0

• r-checkmate

• r-crayon

• r-curl

• r-digest

• r-dplyr

• r-httr

• r-igraph

• r-jsonlite

• r-later

• r-logger

• r-magrittr

• r-progress

• r-purrr

• r-rappdirs

• r-readr >=2.0.0

• r-readxl

• r-rlang

• r-rmarkdown

• r-rvest

• r-stringr

• r-tibble

• r-tidyr

• r-tidyselect

• r-withr

• r-xml2

• r-yaml

Required By:

• bioconductor-wppi

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-omnipathr

and update with:

conda update bioconductor-omnipathr

or 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

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-omnipathr/README.html)