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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 (3.18)

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 163.com>

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

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("PFP")

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

Documentation

Reference Manual PDF

Details

biocViews Pathways, RNASeq, Software
Version 1.9.1
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License GPL-2
Depends R (>= 4.0)
Imports graph, igraph, KEGGgraph, clusterProfiler, ggplot2, plyr, tidyr, magrittr, stats, methods, utils
Linking To
Suggests knitr, testthat, rmarkdown, org.Hs.eg.db
System Requirements
Enhances
URL https://github.com/aib-group/PFP
Bug Reports https://github.com/aib-group/PFP/issues
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/PFP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PFP
Package Short Url https://bioconductor.org/packages/PFP/
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