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 publicationNone
MaintainerWeijun Luo <luo_weijun@yahoo.com>
LicenseGPL (>=3.0)
Version1.14.0
http://pathview.uncc.edu/

View on Bioconductor

Functions

bods Man page
circles Man page
col.key Man page
colorpanel2 Man page
combineKEGGnodes Man page
cpd2kegg Man page
cpd.accs Man page
cpdidmap Man page
cpdkegg2name Man page
cpdname2kegg Man page
cpd.names Man page
cpd.simtypes Man page
demo.paths Man page
download.kegg Man page
eg2id Man page
ellipses Man page
geneannot.map Man page
gene.idtype.bods Man page
gene.idtype.list Man page
gse16873.d Man page
id2eg Man page
KEGGEdgeSubtype Man page
kegg.legend Man page
kegg.met Man page
KEGGpathway2Graph2 Man page
kegg.species.code Man page
keggview.graph Man page
keggview.native Man page
ko.ids Man page
korg Man page
max.abs Man page
mol.sum Man page
node.color Man page
node.info Man page
node.map Man page
parseKGML2Graph2 Man page
parseKGML2.R Man page
parseReaction2 Man page
paths.hsa Man page
pathview Man page
pathview-package Man page
pathview.stamp Man page
random Man page
reaction2edge Man page
rn.list Man page
sim.mol.data Man page
sliced.shapes Man page
strfit Man page
subtypeDisplay.kedge Man page
wordwrap Man page

Files

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/geneannot.map.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.bods.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/paths.hsa.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.pdf
pathview/inst/extdata
pathview/inst/extdata/gse16873.demo
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/tests
pathview/tests/runTests.R
pathview/vignettes
pathview/vignettes/pathview.Rnw
pathview/vignettes/pathview.bib

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