Showing 3 of total 3 results (show query)
egeulgen
pathfindR:Enrichment Analysis Utilizing Active Subnetworks
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>.
Maintained by Ege Ulgen. Last updated 1 months ago.
active-subnetworksenrichmentpathwaypathway-enrichment-analysissubnetwork
187 stars 10.38 score 138 scripts
bioc
ggkegg:Analyzing and visualizing KEGG information using the grammar of graphics
This package aims to import, parse, and analyze KEGG data such as KEGG PATHWAY and KEGG MODULE. The package supports visualizing KEGG information using ggplot2 and ggraph through using the grammar of graphics. The package enables the direct visualization of the results from various omics analysis packages.
Maintained by Noriaki Sato. Last updated 2 months ago.
pathwaysdataimportkeggggplot2ggraphpathwaytidygraphvisualization
225 stars 8.08 score 30 scripts 1 dependentsbioc
BiGGR:Constraint based modeling in R using metabolic reconstruction databases
This package provides an interface to simulate metabolic reconstruction from the BiGG database(http://bigg.ucsd.edu/) and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs.
Maintained by Anand K. Gavai. Last updated 5 months ago.
systems biologypathwaynetworkgraphandnetworkvisualizationmetabolomics
4.67 score 58 scripts