iPath

DOI: 10.18129/B9.bioc.iPath    

iPath pipeline for detecting perturbed pathways at individual level

Bioconductor version: Release (3.14)

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 "4.1") and enter:

if (!requireNamespace("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 1.0.0
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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_1.0.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) iPath_1.0.0.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
Old Source Packages for BioC 3.14 Source Archive

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