pathview

DOI: 10.18129/B9.bioc.pathview    

a tool set for pathway based data integration and visualization

Bioconductor version: Release (3.11)

Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.

Author: Weijun Luo

Maintainer: Weijun Luo <luo_weijun at yahoo.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("pathview")

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("pathview")

 

PDF	R Script	Pathview: pathway based data integration and visualization
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, Genetics, GraphAndNetwork, Metabolomics, Microarray, Pathways, Proteomics, RNASeq, Sequencing, Software, SystemsBiology, Visualization
Version	1.28.1
In Bioconductor since	BioC 2.12 (R-3.0) (7.5 years)
License	GPL (>=3.0)
Depends	R (>= 2.10)
Imports	KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, org.Hs.eg.db, KEGGREST, methods, utils
LinkingTo
Suggests	gage, org.Mm.eg.db, RUnit, BiocGenerics
SystemRequirements
Enhances
URL	https://pathview.uncc.edu/
Depends On Me	BioNetStat, EGSEA, RNASeqR, SBGNview
Imports Me	CompGO, debrowser, EnrichmentBrowser, GDCRNATools, KnowSeq, MAGeCKFlute, TCGAbiolinksGUI, TCGAWorkflow
Suggests Me	CAGEWorkflow, gage, gageData, TCGAbiolinks
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	pathview_1.28.1.tar.gz
Windows Binary	pathview_1.28.1.zip
macOS 10.13 (High Sierra)	pathview_1.28.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/pathview
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pathview
Package Short Url	https://bioconductor.org/packages/pathview/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive