pathview

This is the released version of pathview; for the devel version, see pathview.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12

a tool set for pathway based data integration and visualization

Bioconductor version: Release (3.23)

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>

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

Weijun Luo. pathview: a tool set for pathway based data integration and visualization. doi:10.18129/B9.bioc.pathview, R package version 1.52.0, https://bioconductor.org/packages/pathview.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, Genetics, GraphAndNetwork, Metabolomics, Microarray, Pathways, Proteomics, RNASeq, Sequencing, Software, SystemsBiology, Visualization
Version	1.52.0
In Bioconductor since	BioC 2.12 (R-3.0) (13.5 years)
License	GPL (>=3.0)
Depends	R (>= 3.5.0)
Imports	KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, org.Hs.eg.db, KEGGREST, methods, utils
System Requirements
URL	https://github.com/datapplab/pathview https://pathview.uncc.edu/

Suggests	gage, org.Mm.eg.db, RUnit, BiocGenerics
Linking To
Enhances
Depends On Me	EGSEA, SBGNview
Imports Me	debrowser, EnrichmentBrowser, GDCRNATools, lilikoi, SQMtools
Suggests Me	CAGEWorkflow, gage, gageData, ReporterScore, TCGAbiolinks
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	pathview_1.52.0.tar.gz
Windows Binary (x86_64)	pathview_1.52.0.zip
macOS Binary (big-sur-x86_64)	pathview_1.52.0.tgz
macOS Binary (sonoma-arm64)	pathview_1.52.0.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