Package: iPath
Type: Package
Title: iPath pipeline for detecting perturbed pathways at individual
        level
Version: 1.0.0
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
git_url: https://git.bioconductor.org/packages/iPath
git_branch: RELEASE_3_14
git_last_commit: 10fca6d
git_last_commit_date: 2021-10-26
Date/Publication: 2021-10-26
Packaged: 2021-10-26 21:44:02 UTC; biocbuild
Author: Kenong Su [aut, cre],
  Zhaohui Qin [aut]
Maintainer: Kenong Su <kenong.su@emory.edu>
Built: R 4.1.2; x86_64-conda-linux-gnu; 2022-02-24 13:36:49 UTC; unix
