PFP

DOI: 10.18129/B9.bioc.PFP    

This is the development version of PFP; to use it, please install the devel version of Bioconductor.

Pathway Fingerprint Framework in R

Bioconductor version: Development (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>

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

Installation

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

if (!requireNamespace("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

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 0.99.12
In Bioconductor since BioC 3.13 (R-4.1)
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_0.99.12.tar.gz
Windows Binary PFP_0.99.12.zip
macOS 10.13 (High Sierra) PFP_0.99.12.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

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