Package: PoTRA
Type: Package
Title: PoTRA: Pathways of Topological Rank Analysis
Version: 1.12.0
Author: Chaoxing Li, Li Liu and Valentin Dinu
Maintainer: Margaret Linan <mlinan@asu.edu>
Description: The PoTRA analysis is based on topological ranks of genes in biological pathways. PoTRA can be used to detect pathways involved in disease (Li, Liu & Dinu, 2018). We use PageRank to measure the relative topological ranks of genes in each biological pathway, then select hub genes for each pathway, and use Fishers Exact test to determine if the number of hub genes in each pathway is altered from normal to cancer (Li, Liu & Dinu, 2018). Alternatively, if the distribution of topological ranks of gene in a pathway is altered between normal and cancer, this pathway might also be involved in cancer (Li, Liu & Dinu, 2018). Hence, we use the Kolmogorov–Smirnov test to detect pathways that have an altered distribution of topological ranks of genes between two phenotypes (Li, Liu & Dinu, 2018). PoTRA can be used with the KEGG, Reactome, SMPDB and PharmGKB, Panther, PathBank, etc databases from the devel graphite library.   
License: LGPL
Encoding: UTF-8
Depends: R (>= 3.6.0), stats, BiocGenerics, org.Hs.eg.db, igraph,
        graph, graphite
Imports:
biocViews: GraphAndNetwork, StatisticalMethod, GeneExpression,
        DifferentialExpression, Pathways, Reactome, Network, KEGG,
        PathBank, Panther
RoxygenNote: 6.1.1
Suggests: BiocStyle, knitr, rmarkdown, colr, metap, repmis
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/PoTRA
git_branch: RELEASE_3_15
git_last_commit: 23ce63f
git_last_commit_date: 2022-04-26
Date/Publication: 2022-04-26
NeedsCompilation: no
Packaged: 2022-04-27 00:29:57 UTC; biocbuild
Built: R 4.2.0; ; 2022-04-27 09:54:08 UTC; windows
