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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 (from within R, enter 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 PDF
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
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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