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a tool set for pathway based data integration and visualization

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, Genetics, GraphAndNetwork, Metabolomics, Microarray, Pathways, Proteomics, RNASeq, Sequencing, Software, SystemsBiology, Visualization
Version 1.44.0
In Bioconductor since BioC 2.12 (R-3.0) (11.5 years)
License GPL (>=3.0)
Depends R (>= 3.5.0)
Imports KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi,, KEGGREST, methods, utils
System Requirements
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Suggests gage,,, RUnit, BiocGenerics
Linking To
Depends On Me EGSEA, SBGNview
Imports Me debrowser, EnrichmentBrowser, GDCRNATools, MAGeCKFlute, TCGAWorkflow, lilikoi, SQMtools
Suggests Me gage, TCGAbiolinks, gageData, CAGEWorkflow, ReporterScore
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package pathview_1.44.0.tar.gz
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macOS Binary (x86_64) pathview_1.44.0.tgz
macOS Binary (arm64) pathview_1.44.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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