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PFP

Pathway Fingerprint Framework in R

Bioconductor version: Release (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

Details

biocViews Pathways, RNASeq, Software
Version 1.7.0
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
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
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