QuaternaryProd
This is the development version of QuaternaryProd; for the stable release version, see QuaternaryProd.
Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs
Bioconductor version: Development (3.24)
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.
Author: Carl Tony Fakhry [cre, aut], Ping Chen [ths], Kourosh Zarringhalam [aut, ths]
Maintainer: Carl Tony Fakhry <cfakhry at cs.umb.edu>
citation("QuaternaryProd")):Carl Tony Fakhry, Kourosh Zarringhalam. QuaternaryProd: Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs. doi:10.18129/B9.bioc.QuaternaryProd, R package version 1.47.0, https://bioconductor.org/packages/QuaternaryProd.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("QuaternaryProd")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("QuaternaryProd")| <span style="color:red">QuaternaryProdVignette</span> | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GraphAndNetwork, Software, Transcription |
| Version | 1.47.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | GPL (>=3) |
| Depends | R (>= 3.2.0), Rcpp (>= 0.11.3), dplyr, yaml (>= 2.1.18) |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | knitr |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | QuaternaryProd_1.47.0.tar.gz |
| Windows Binary (x86_64) | QuaternaryProd_1.47.0.zip |
| macOS Binary (big-sur-x86_64) | QuaternaryProd_1.47.0.tgz |
| macOS Binary (sonoma-arm64) | QuaternaryProd_1.47.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/QuaternaryProd |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/QuaternaryProd |
| Package Short Url | https://bioconductor.org/packages/QuaternaryProd/ |
| Package Downloads Report | Download Stats |