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pathview

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 yahoo.com>

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

Installation

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

Details

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 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/
See More
Suggests gage, org.Mm.eg.db, org.EcK12.eg.db, RUnit, BiocGenerics
Linking To
Enhances
Depends On Me EGSEA, SBGNview
Imports Me debrowser, EnrichmentBrowser, GDCRNATools, MAGeCKFlute, TCGAWorkflow, lilikoi, SQMtools
Suggests Me gage, TCGAbiolinks, gageData, CAGEWorkflow, ReporterScore
Links To Me
Build Report Build Report

Package Archives

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

Source Package pathview_1.44.0.tar.gz
Windows Binary pathview_1.44.0.zip
macOS Binary (x86_64) pathview_1.44.0.tgz
macOS Binary (arm64) pathview_1.44.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pathview
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pathview
Bioc Package Browser https://code.bioconductor.org/browse/pathview/
Package Short Url https://bioconductor.org/packages/pathview/
Package Downloads Report Download Stats