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>

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

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

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