pathview: a tool set for pathway based data integration and visualization

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.

AuthorWeijun Luo
Date of publication2014-04-07 19:48:22
MaintainerWeijun Luo <luo_weijun@yahoo.com>
LicenseGPL (>=3.0)
Version1.3.5
http://pathview.r-forge.r-project.org/

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Files in this package

pathview/DESCRIPTION
pathview/NAMESPACE
pathview/NEWS
pathview/R
pathview/R/KEGGpathway2Graph2.R pathview/R/circles.R pathview/R/col.key.R pathview/R/colorpanel2.R pathview/R/combineKEGGnodes.R pathview/R/cpd2kegg.R pathview/R/cpdidmap.R pathview/R/cpdkegg2name.R pathview/R/cpdname2kegg.R pathview/R/download.kegg.R pathview/R/eg2id.R pathview/R/ellipses.R pathview/R/id2eg.R pathview/R/kegg.legend.R pathview/R/kegg.species.code.R pathview/R/keggview.graph.R pathview/R/keggview.native.R pathview/R/max.abs.R pathview/R/mol.sum.R pathview/R/node.color.R pathview/R/node.info.R pathview/R/node.map.R pathview/R/parseKGML2.R pathview/R/parseKGML2Graph2.R pathview/R/parseReaction2.R pathview/R/pathview.R pathview/R/pathview.stamp.R pathview/R/random.R pathview/R/reaction2edge.R pathview/R/render.kegg.node.R pathview/R/sim.mol.data.R pathview/R/sliced.shapes.R pathview/R/strfit.R pathview/R/subtypeDisplay.kedge.R pathview/R/wordwrap.R pathview/R/zzz.R
pathview/build
pathview/build/vignette.rds
pathview/data
pathview/data/KEGGEdgeSubtype.rda
pathview/data/bods.rda
pathview/data/cpd.accs.rda
pathview/data/cpd.names.rda
pathview/data/cpd.simtypes.rda
pathview/data/datalist
pathview/data/demo.paths.rda
pathview/data/gene.idtype.list.rda
pathview/data/gse16873.d.rda
pathview/data/kegg.met.rda
pathview/data/ko.ids.rda
pathview/data/korg.rda
pathview/data/rn.list.rda
pathview/inst
pathview/inst/CITATION
pathview/inst/doc
pathview/inst/doc/pathview.R
pathview/inst/doc/pathview.Rnw
pathview/inst/doc/pathview.bib
pathview/inst/doc/pathview.pdf
pathview/inst/extdata
pathview/inst/extdata/hsa04110.png
pathview/inst/extdata/hsa04110.xml
pathview/inst/extdata/kegg.sigmet.rda
pathview/inst/unitTests
pathview/inst/unitTests/test_mapper.R
pathview/man
pathview/man/combineKEGGnodes.Rd pathview/man/cpd.accs.Rd pathview/man/cpdidmap.Rd pathview/man/demo.data.Rd pathview/man/download.kegg.Rd pathview/man/eg2id.Rd pathview/man/kegg.species.code.Rd pathview/man/korg.Rd pathview/man/mol.sum.Rd pathview/man/node.color.Rd pathview/man/node.info.Rd pathview/man/node.map.Rd pathview/man/pathview-internal.Rd pathview/man/pathview-package.Rd pathview/man/pathview.Rd pathview/man/sim.mol.data.Rd pathview/man/wordwrap.Rd
pathview/test
pathview/tests
pathview/tests/runTests.R

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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