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

Quantify deregulation of pathways in cancer

Bioconductor version: Development (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews Network, Software
Version 1.43.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License Artistic-1.0
Imports R.oo, princurve (>= 2.0.4)
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