pathifier

DOI: 10.18129/B9.bioc.pathifier    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see pathifier.

Quantify deregulation of pathways in cancer

Bioconductor version: 3.12

Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.

Author: Yotam Drier

Maintainer: Assif Yitzhaky <assif.yitzhaky at weizmann.ac.il>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("pathifier")

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("pathifier")

 

PDF	R Script	Quantify deregulation of pathways in cancer
PDF		Reference Manual

Details

biocViews	Network, Software
Version	1.28.0
In Bioconductor since	BioC 2.13 (R-3.0) (7.5 years)
License	Artistic-1.0
Depends
Imports	R.oo, princurve (>= 2.0.4)
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	lilikoi
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	pathifier_1.28.0.tar.gz
Windows Binary	pathifier_1.28.0.zip
macOS 10.13 (High Sierra)	pathifier_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/pathifier
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pathifier
Package Short Url	https://bioconductor.org/packages/pathifier/
Package Downloads Report	Download Stats