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SourceSet  

A Graphical Model Approach to Identify Primary Genes in Perturbed Biological Pathways
View on CRAN: Click here


Download and install SourceSet package within the R console
Install from CRAN:
install.packages("SourceSet")

Install from Github:
library("remotes")
install_github("cran/SourceSet")

Install by package version:
library("remotes")
install_version("SourceSet", "0.1.5")



Attach the package and use:
library("SourceSet")
Maintained by
Elisa Salviato
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-02-28
Latest Update: 2023-10-06
Description:
The algorithm pursues the identification of the set of variables driving the differences in two different experimental conditions (i.e., the primary genes) within a graphical model context. It uses the idea of simultaneously looking for the differences between two multivariate normal distributions in all marginal and conditional distributions associated with a decomposable graph, which represents the pathway under exam. The implementation accommodates genomics specific issues (low sample size and multiple testing issues) and provides a number of functions offering numerical and visual summaries to help the user interpret the obtained results. In order to use the (optional) 'Cytoscape' functionalities, the suggested 'r2cytoscape' package must be installed from the 'GitHub' repository ('devtools::install_github('cytoscape/r2cytoscape')'). More details in Salviato et al., (2020) and Djordjilovic et al., (2022) .
How to cite:
Elisa Salviato (2018). SourceSet: A Graphical Model Approach to Identify Primary Genes in Perturbed Biological Pathways. R package version 0.1.5, https://cran.r-project.org/web/packages/SourceSet. Accessed 21 Dec. 2024.
Previous versions and publish date:
0.1.0 (2018-02-28 18:36), 0.1.1 (2018-04-24 10:01), 0.1.3 (2019-10-19 00:00), 0.1.5 (2022-11-21 12:30)
Other packages that cited SourceSet R package
View SourceSet citation profile
Other R packages that SourceSet depends, imports, suggests or enhances
Functions, R codes and Examples using the SourceSet R package
Some associated functions: easyLookSource . getPermutations . infoSource . parameters . ripAllRootsClique . shrinkTEGS . simulation . sourceCytoscape . sourceSankeyDiagram . sourceSet . sourceUnionCytoscape . testMeanVariance . 
Some associated R codes: mainFunctions.R .  Full SourceSet package functions and examples
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