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This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
Bioconductor version: Release (3.18)
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")
):
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.
Reference Manual |
biocViews | Pathways, RNASeq, Software |
Version | 1.10.0 |
In Bioconductor since | BioC 3.13 (R-4.1) (2.5 years) |
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 |
Follow Installation instructions to use this package in your R session.
Source Package | |
Windows Binary | |
macOS Binary (x86_64) | |
macOS Binary (arm64) | |
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 |
Old Source Packages for BioC 3.18 | Source Archive |
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