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pathifier

This is the development version of pathifier; for the stable release version, see pathifier.

Quantify deregulation of pathways in cancer

Bioconductor version: Development (3.18)

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>

Citation (from within R, enter citation("pathifier")):

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Network, Software
Version 1.39.0
In Bioconductor since BioC 2.13 (R-3.0) (10 years)
License Artistic-1.0
Depends
Imports R.oo, princurve (>= 2.0.4)
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Package Archives

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

Source Package pathifier_1.39.0.tar.gz
Windows Binary pathifier_1.39.0.zip
macOS Binary (x86_64) pathifier_1.39.0.tgz
macOS Binary (arm64) pathifier_1.39.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pathifier
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pathifier
Bioc Package Browser https://code.bioconductor.org/browse/pathifier/
Package Short Url https://bioconductor.org/packages/pathifier/
Package Downloads Report Download Stats