PFP

DOI: 10.18129/B9.bioc.PFP    

Pathway Fingerprint Framework in R

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	Pathways, RNASeq, Software
Version	1.0.0
In Bioconductor since	BioC 3.13 (R-4.1) (< 6 months)
License	GPL-2
Depends	R (>= 4.0)
Imports	graph, igraph, KEGGgraph, clusterProfiler, ggplot2, plyr, tidyr, magrittr, stats, methods, utils
LinkingTo
Suggests	knitr, testthat, rmarkdown, org.Hs.eg.db
SystemRequirements
Enhances
URL	https://github.com/aib-group/PFP
BugReports	https://github.com/aib-group/PFP/issues
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_1.0.0.tar.gz
Windows Binary	PFP_1.0.0.zip
macOS 10.13 (High Sierra)	PFP_1.0.0.tgz
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/
Package Downloads Report	Download Stats