iPath
iPath pipeline for detecting perturbed pathways at individual level
Bioconductor version: Release (3.17)
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("iPath")):
Installation
To install this package, start R (version "4.3") 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.
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 |
Details
| biocViews | GeneExpression, Pathways, Software, Survival |
| Version | 1.6.1 |
| In Bioconductor since | BioC 3.14 (R-4.1) (2 years) |
| License | GPL-2 |
| Depends | R (>= 4.1), mclust, BiocParallel, survival |
| Imports | Rcpp (>= 1.0.5), matrixStats, ggpubr, ggplot2, survminer, stats |
| Linking To | Rcpp, RcppArmadillo |
| Suggests | rmarkdown, BiocStyle, knitr |
| System Requirements | C++11 |
| Enhances | |
| URL | |
| Bug Reports | https://github.com/suke18/iPath/issues |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | iPath_1.6.1.tar.gz |
| Windows Binary | iPath_1.6.1.zip |
| macOS Binary (x86_64) | iPath_1.6.1.tgz |
| macOS Binary (arm64) | iPath_1.6.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/iPath |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/iPath |
| Bioc Package Browser | https://code.bioconductor.org/browse/iPath/ |
| Package Short Url | https://bioconductor.org/packages/iPath/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.17 | Source Archive |