iPath
This is the released version of iPath; for the devel version, see iPath.
All Bioconductor versions of iPath
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14
iPath pipeline for detecting perturbed pathways at individual level
Bioconductor version: 3.23 · Package version: 1.18.0
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.
Author: Kenong Su [aut, cre], Zhaohui Qin [aut]
Maintainer: Kenong Su <kenong.su at emory.edu>
Citation
From within R, enter citation("iPath"):
Kenong Su, Zhaohui Qin. iPath: iPath pipeline for detecting perturbed pathways at individual level. doi:10.18129/B9.bioc.iPath, R package version 1.18.0, https://bioconductor.org/packages/iPath.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("iPath")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.18.0 |
| License | GPL-2 |
| Bug Reports | https://github.com/suke18/iPath/issues |
| System Requirements | C++11 |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.14 (R-4.1) (4 years) |
| Downloads rank | 2105 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, Pathways, Software, Survival |
| Package Short Url | https://bioconductor.org/packages/iPath/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("iPath")| The iPath User's Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | iPath_1.18.0.tar.gz |
| macOS binary (arm64) | iPath_1.18.0.tgz |
| macOS binary (x86_64) | iPath_1.18.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/iPath |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/iPath |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.1), mclust, BiocParallel, survival
Imports: Rcpp (>= 1.0.5), matrixStats, ggpubr, ggplot2, survminer, stats
LinkingTo: Rcpp, RcppArmadillo