pathview

a tool set for pathway based data integration and visualization

Bioconductor version: Release (2.14)

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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("pathview")

To cite this package in a publication, start R and enter:

    citation("pathview")

Documentation

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

Details

biocViews Bioinformatics, DifferentialExpression, GeneExpression, GeneSetEnrichment, Genetics, GraphsAndNetworks, Metabolomics, Microarray, NetworkVisualization, Pathways, Proteomics, RNAseq, Software
Version 1.4.0
In Bioconductor since BioC 2.12 (R-3.0)
License GPL (>=3.0)
Depends R (>= 2.10), KEGGgraph, org.Hs.eg.db
Imports Rgraphviz, graph, png, AnnotationDbi, KEGGREST, methods, utils
Suggests gage, org.Mm.eg.db, RUnit, BiocGenerics
System Requirements
URL http://pathview.r-forge.r-project.org/
Depends On Me
Imports Me
Suggests Me clusterProfiler, gage, gageData

Package Downloads

Package Source pathview_1.4.0.tar.gz
Windows Binary pathview_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) pathview_1.4.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

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