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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>.

Type Size Name Uploaded Downloads Labels
conda 2.1 MB | noarch/r-pathfindr-2.5.1-r44h3121a25_0.tar.bz2  20 days and 53 minutes ago 27 main
conda 2.2 MB | noarch/r-pathfindr-2.5.0-r44h3121a25_0.tar.bz2  1 month and 20 days ago 74 main
conda 2.2 MB | noarch/r-pathfindr-2.4.2-r44h3121a25_0.tar.bz2  5 months and 18 days ago 192 main
conda 2.4 MB | noarch/r-pathfindr-2.4.1-r43h3121a25_0.tar.bz2  1 year and 2 months ago 757 main
conda 2.3 MB | noarch/r-pathfindr-2.4.0-r43h3121a25_0.tar.bz2  1 year and 3 months ago 728 main
conda 3.0 MB | noarch/r-pathfindr-2.3.1-r43h3342da4_0.tar.bz2  1 year and 6 months ago 945 main
conda 3.0 MB | noarch/r-pathfindr-2.3.0-r43h3342da4_0.tar.bz2  1 year and 9 months ago 1129 main
conda 3.0 MB | noarch/r-pathfindr-2.2.0-r43h3342da4_0.tar.bz2  1 year and 11 months ago 1221 main
conda 3.0 MB | noarch/r-pathfindr-2.1.0-r43h3342da4_0.tar.bz2  1 year and 11 months ago 1228 main

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