- recipe bioconductor-paxtoolsr
Access Pathways from Multiple Databases Through BioPAX and Pathway Commons
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/paxtoolsr.html
- License:
LGPL-3
- Recipe:
The package provides a set of R functions for interacting with BioPAX OWL files using Paxtools and the querying Pathway Commons (PC) molecular interaction database. Pathway Commons is a project by the Memorial Sloan-Kettering Cancer Center (MSKCC), Dana-Farber Cancer Institute (DFCI), and the University of Toronto. Pathway Commons databases include: BIND, BioGRID, CORUM, CTD, DIP, DrugBank, HPRD, HumanCyc, IntAct, KEGG, MirTarBase, Panther, PhosphoSitePlus, Reactome, RECON, TRANSFAC.
- package bioconductor-paxtoolsr¶
- Versions:
1.36.0-0,1.34.0-0,1.32.0-0,1.28.0-0,1.26.0-0,1.24.0-1,1.24.0-0,1.20.0-0,1.18.0-1,1.36.0-0,1.34.0-0,1.32.0-0,1.28.0-0,1.26.0-0,1.24.0-1,1.24.0-0,1.20.0-0,1.18.0-1,1.18.0-0,1.16.0-0- Depends:
on openjdk
on r-base
>=4.3,<4.4.0a0on r-httr
on r-igraph
on r-jsonlite
on r-plyr
on r-r.utils
on r-rappdirs
on r-readr
on r-rjava
>=0.9-8on r-rjson
on r-xml
- 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-paxtoolsr
to add into an existing workspace instead, run:
pixi add bioconductor-paxtoolsr
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-paxtoolsr
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-paxtoolsr
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-paxtoolsr:<tag>
(see bioconductor-paxtoolsr/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:
[](http://bioconda.github.io/recipes/bioconductor-paxtoolsr/README.html)
