PFP
This package is for version 3.16 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: 3.16
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("PFP")):
Installation
To install this package, start R (version "4.2") 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 | ||
| NEWS | Text |
Details
| biocViews | Pathways, RNASeq, Software |
| Version | 1.6.0 |
| 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 |
See More
| 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_1.6.0.tar.gz |
| Windows Binary | PFP_1.6.0.zip |
| macOS Binary (x86_64) | PFP_1.6.0.tgz |
| macOS Binary (arm64) | PFP_1.6.0.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 3.16 | Source Archive |