- recipe bioconductor-quaternaryprod
Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/QuaternaryProd.html
- License:
GPL (>=3)
- Recipe:
- Links:
biotools: quaternaryprod
QuaternaryProd is an R package that performs causal reasoning on biological networks, including publicly available networks such as STRINGdb. QuaternaryProd is an open-source alternative to commercial products such as Inginuity Pathway Analysis. For a given a set of differentially expressed genes, QuaternaryProd computes the significance of upstream regulators in the network by performing causal reasoning using the Quaternary Dot Product Scoring Statistic (Quaternary Statistic), Ternary Dot product Scoring Statistic (Ternary Statistic) and Fisher's exact test (Enrichment test). The Quaternary Statistic handles signed, unsigned and ambiguous edges in the network. Ambiguity arises when the direction of causality is unknown, or when the source node (e.g., a protein) has edges with conflicting signs for the same target gene. On the other hand, the Ternary Statistic provides causal reasoning using the signed and unambiguous edges only. The Vignette provides more details on the Quaternary Statistic and illustrates an example of how to perform causal reasoning using STRINGdb.
- package bioconductor-quaternaryprod¶
- Versions:
1.44.0-0,1.40.0-0,1.36.0-0,1.34.0-0,1.32.0-2,1.32.0-1,1.32.0-0,1.28.0-2,1.28.0-1,1.44.0-0,1.40.0-0,1.36.0-0,1.34.0-0,1.32.0-2,1.32.0-1,1.32.0-0,1.28.0-2,1.28.0-1,1.28.0-0,1.26.0-0,1.24.0-1,1.24.0-0,1.22.0-0,1.20.0-0,1.18.0-1,1.18.0-0,1.16.0-0,1.14.0-0,1.6.0-0- Depends:
on libblas
>=3.9.0,<4.0a0on libgcc
>=14on liblapack
>=3.9.0,<4.0a0on liblzma
>=5.8.2,<6.0a0on libstdcxx
>=14on libzlib
>=1.3.1,<2.0a0on r-base
>=4.5,<4.6.0a0on r-dplyr
on r-rcpp
>=0.11.3on r-yaml
>=2.1.18
- 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-quaternaryprod
to add into an existing workspace instead, run:
pixi add bioconductor-quaternaryprod
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-quaternaryprod
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-quaternaryprod
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-quaternaryprod:<tag>
(see bioconductor-quaternaryprod/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-quaternaryprod/README.html)
