- recipe r-pathfindr
Enrichment analysis enables researchers to uncover mechanisms underlying a phenotype. However, conventional methods for enrichment analysis do not take into account protein-protein interaction information, resulting in incomplete conclusions. pathfindR is a tool for enrichment analysis utilizing active subnetworks. The main function identifies active subnetworks in a protein-protein interaction network using a user-provided list of genes and associated p values. It then performs enrichment analyses on the identified subnetworks, identifying enriched terms (i.e. pathways or, more broadly, gene sets) that possibly underlie the phenotype of interest. pathfindR also offers functionalities to cluster the enriched terms and identify representative terms in each cluster, to score the enriched terms per sample and to visualize analysis results. The enrichment, clustering and other methods implemented in pathfindR are described in detail in Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. Front. Genet. <doi:10.3389/fgene.2019.00858>.
- Homepage:
- Documentation:
- License:
MIT / MIT
- Recipe:
- package r-pathfindr¶
- Versions:
2.7.0-0,2.6.0-0,2.5.1-0,2.5.0-0,2.4.2-0,2.4.1-0,2.4.0-0,2.3.1-0,2.3.0-0,2.7.0-0,2.6.0-0,2.5.1-0,2.5.0-0,2.4.2-0,2.4.1-0,2.4.0-0,2.3.1-0,2.3.0-0,2.2.0-0,2.1.0-0- Depends:
on bioconductor-annotationdbi
on bioconductor-ggkegg
on bioconductor-kegggraph
on bioconductor-keggrest
on bioconductor-org.hs.eg.db
on openjdk
8.*on r-base
>=4.4,<4.5.0a0on r-dbi
on r-doparallel
on r-foreach
on r-fpc
on r-ggplot2
on r-ggraph
on r-ggupset
on r-httr
on r-igraph
on r-knitr
on r-magick
on r-msigdbr
on r-pathfindr.data
>=2.0on r-r.utils
on r-rmarkdown
- 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 r-pathfindr
to add into an existing workspace instead, run:
pixi add r-pathfindr
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 r-pathfindr
Alternatively, to install into a new environment, run:
conda create -n envname r-pathfindr
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/r-pathfindr:<tag>
(see r-pathfindr/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/r-pathfindr/README.html)
