This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

pathifier

Quantify deregulation of pathways in cancer

Bioconductor version: Release (3.17)

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")

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 1.38.0
In Bioconductor since BioC 2.13 (R-3.0) (10 years)
License Artistic-1.0
Depends
Imports R.oo, princurve (>= 2.0.4)
Linking To
Suggests
System Requirements
Enhances
URL
See More
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 pathifier_1.38.0.tar.gz
Windows Binary pathifier_1.38.0.zip
macOS Binary (x86_64) pathifier_1.38.0.tgz
macOS Binary (arm64) pathifier_1.38.0.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