pathifier
This is the released version of pathifier; for the devel version, see pathifier.
All Bioconductor versions of pathifier
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13
Quantify deregulation of pathways in cancer
Bioconductor version: 3.23 · Package version: 1.50.0
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"):
Yotam Drier. pathifier: Quantify deregulation of pathways in cancer. doi:10.18129/B9.bioc.pathifier, R package version 1.50.0, https://bioconductor.org/packages/pathifier.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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.
Details
| Version | 1.50.0 |
| License | Artistic-1.0 |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 2.13 (R-3.0) (12 years) |
| Downloads rank | 1394 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Network, Software |
| Package Short Url | https://bioconductor.org/packages/pathifier/ |
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 | R Script | |
| Reference Manual |
Download
Follow the installation instructions to use this package in your R session.
| Source package | pathifier_1.50.0.tar.gz |
| Windows binary (x86_64) | pathifier_1.50.0.zip |
| macOS binary (arm64) | pathifier_1.50.0.tgz |
| macOS binary (x86_64) | pathifier_1.50.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/pathifier |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/pathifier |
| Package Downloads Report | Download Stats |
Dependencies
Imports: R.oo, princurve (>= 2.0.4)
Reverse dependencies
Imports Me (1): funOmics