iPath

DOI: 10.18129/B9.bioc.iPath    

iPath pipeline for detecting perturbed pathways at individual level

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	The iPath User's Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, Pathways, Software, Survival
Version	1.2.0
In Bioconductor since	BioC 3.14 (R-4.1) (1 year)
License	GPL-2
Depends	R (>= 4.1), mclust, BiocParallel, survival
Imports	Rcpp (>= 1.0.5), matrixStats, ggpubr, ggplot2, survminer, stats
LinkingTo	Rcpp, RcppArmadillo
Suggests	rmarkdown, BiocStyle, knitr
SystemRequirements	C++11
Enhances
URL
BugReports	https://github.com/suke18/iPath/issues
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_1.2.0.tar.gz
Windows Binary	iPath_1.2.0.zip
macOS Binary (x86_64)	iPath_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/iPath
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/iPath
Package Short Url	https://bioconductor.org/packages/iPath/
Package Downloads Report	Download Stats