PFP

This package is for version 3.17 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see PFP.

Pathway Fingerprint Framework in R

Bioconductor version: 3.17

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")

BiocManager::install("PFP")

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("PFP")

Pathway fingerprint: a tool for biomarker discovery based on gene expression data and pathway knowledge	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Pathways, RNASeq, Software
Version	1.7.0
In Bioconductor since	BioC 3.13 (R-4.1) (3 years)
License	GPL-2
Depends	R (>= 4.0)
Imports	graph, igraph, KEGGgraph, clusterProfiler, ggplot2, plyr, tidyr, magrittr, stats, methods, utils
System Requirements
URL	https://github.com/aib-group/PFP
Bug Reports	https://github.com/aib-group/PFP/issues

Suggests	knitr, testthat, rmarkdown, org.Hs.eg.db
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	PFP_1.7.0.tar.gz
Windows Binary	PFP_1.7.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)	PFP_1.7.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PFP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/PFP
Bioc Package Browser	https://code.bioconductor.org/browse/PFP/
Package Short Url	https://bioconductor.org/packages/PFP/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive