Package Recipe 'bioconductor-omnipathr'

recipe bioconductor-omnipathr

OmniPath web service client and more

Homepage:: https://bioconductor.org/packages/3.20/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:

3.18.4-0, 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,

3.18.4-0, 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:

on r-base >=4.5,<4.6.0a0
on r-checkmate
on r-crayon
on r-curl
on r-digest
on r-dplyr >=1.1.0
on r-fs
on r-httr2
on r-igraph
on r-jsonlite
on r-later
on r-logger
on r-lubridate
on r-magrittr
on r-progress
on r-purrr
on r-r.utils
on r-rappdirs
on r-readr >=2.0.0
on r-readxl
on r-rlang
on r-rmarkdown
on r-rsqlite
on r-rvest
on r-sessioninfo
on r-stringi
on r-stringr
on r-tibble
on r-tidyr
on r-tidyselect
on r-vctrs
on r-withr
on r-xml
on r-xml2
on r-yaml
on r-zip

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-omnipathr

to add into an existing workspace instead, run:

pixi add bioconductor-omnipathr

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-omnipathr

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-omnipathr

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-omnipathr:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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)