DOI: 10.18129/B9.bioc.PFP  

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

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

Pathway Fingerprint Framework in R

Bioconductor version: Development (3.19)

An implementation of the pathway fingerprint framework that introduced in paper "Pathway Fingerprint: a novel pathway knowledge and topology based method for biomarker discovery and characterization". This method provides a systematic comparisons between a gene set (such as a list of differentially expressed genes) and well-studied "basic pathway networks" (KEGG pathways), measuring the importance of pathways and genes for the gene set. The package is helpful for researchers to find the biomarkers and its function.

Author: XC Zhang [aut, cre]

Maintainer: XC Zhang <kunghero at>

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


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.


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biocViews Pathways, RNASeq, Software
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (2.5 years)
License GPL-2
Depends R (>= 4.0)
Imports graph, igraph, KEGGgraph, clusterProfiler, ggplot2, plyr, tidyr, magrittr, stats, methods, utils
Suggests knitr, testthat, rmarkdown,
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