Package: iPath
Type: Package
Title: iPath pipeline for detecting perturbed pathways at individual
        level
Version: 1.18.0
Authors@R: c(person("Kenong","Su", email ="kenong.su@emory.edu", role = c("aut","cre")),
            person("Zhaohui","Qin", email ="zhaohui.qin@emory.edu", role ="aut"))
Description: iPath is the Bioconductor package used for calculating
        personalized pathway score and test the association with
        survival outcomes. Abundant single-gene biomarkers have been
        identified and used in the clinics. However, hundreds of
        oncogenes or tumor-suppressor genes are involved during the
        process of tumorigenesis. We believe individual-level
        expression patterns of pre-defined pathways or gene sets are
        better biomarkers than single genes. In this study, we devised
        a computational method named iPath to identify prognostic
        biomarker pathways, one sample at a time. To test its utility,
        we conducted a pan-cancer analysis across 14 cancer types from
        The Cancer Genome Atlas and demonstrated that iPath is capable
        of identifying highly predictive biomarkers for clinical
        outcomes, including overall survival, tumor subtypes, and tumor
        stage classifications. We found that pathway-based biomarkers
        are more robust and effective than single genes.
License: GPL-2
Encoding: UTF-8
Suggests: rmarkdown, BiocStyle, knitr
VignetteBuilder: knitr
Imports: Rcpp (>= 1.0.5), matrixStats, ggpubr, ggplot2, survminer,
        stats
biocViews: Pathways, Software, GeneExpression, Survival
NeedsCompilation: yes
SystemRequirements: C++11
LinkingTo: Rcpp, RcppArmadillo
Depends: R (>= 4.1), mclust, BiocParallel, survival
RoxygenNote: 7.1.1
BugReports: https://github.com/suke18/iPath/issues
Config/pak/sysreqs: cmake make libicu-dev libjpeg-dev libpng-dev
        libxml2-dev libssl-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:56:34 UTC
RemoteUrl: https://github.com/bioc/iPath
RemoteRef: RELEASE_3_23
RemoteSha: 350074a9dd4698e109eedcaf20d60fdb2b8952d2
Packaged: 2026-04-29 22:27:29 UTC; root
Author: Kenong Su [aut, cre],
  Zhaohui Qin [aut]
Maintainer: Kenong Su <kenong.su@emory.edu>
Built: R 4.6.0; x86_64-apple-darwin20; 2026-04-29 23:03:22 UTC; unix
