Cite our work | Quick start with demo data | New features | Overview | Installation | Get Started | Common uses for data visualization | Data integration | Integrated workflow with pathway analysis | Common Errors
Package: pathview 1.53.0
Weijun Luo
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.
Authors:
pathview_1.53.0.tar.gz
pathview_1.53.0.zip(r-4.7)pathview_1.53.0.zip(r-4.6)pathview_1.53.0.zip(r-4.5)
pathview_1.53.0.tgz(r-4.6-any)pathview_1.53.0.tgz(r-4.5-any)
pathview_1.53.0.tar.gz(r-4.7-any)pathview_1.53.0.tar.gz(r-4.6-any)
pathview_1.53.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
pathview/json (API)
| # Install 'pathview' in R: |
| install.packages('pathview', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/datapplab/pathview/issues
Datasets:
- bods - Mapping data on KEGG species code and corresponding Bioconductor gene annotation package
- cpd.accs - Mapping data between compound or gene IDs and KEGG accessions
- cpd.names - Mapping data between compound or gene IDs and KEGG accessions
- cpd.simtypes - Mapping data between compound or gene IDs and KEGG accessions
- demo.paths - Data for demo purpose
- gene.idtype.bods - Mapping data between compound or gene IDs and KEGG accessions
- gene.idtype.list - Mapping data between compound or gene IDs and KEGG accessions
- gse16873.d - Data for demo purpose
- kegg.met - Mapping data between compound or gene IDs and KEGG accessions
- ko.ids - Mapping data between compound or gene IDs and KEGG accessions
- korg - Mapping data on KEGG species code and corresponding Bioconductor gene annotation package
- paths.hsa - Data for demo purpose
- rn.list - Mapping data between compound or gene IDs and KEGG accessions
On BioConductor:pathview-1.53.0(bioc 3.24)pathview-1.52.0(bioc 3.23)
pathwaysgraphandnetworkvisualizationgenesetenrichmentdifferentialexpressiongeneexpressionmicroarrayrnaseqgeneticsmetabolomicsproteomicssystemsbiologysequencing
Last updated from:0bcc04371e. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 198 | ||
| linux-devel-x86_64 | WARNING | 435 | ||
| source / vignettes | OK | 361 | ||
| linux-release-x86_64 | WARNING | 418 | ||
| macos-release-arm64 | WARNING | 273 | ||
| macos-oldrel-arm64 | WARNING | 242 | ||
| windows-devel | WARNING | 239 | ||
| windows-release | WARNING | 242 | ||
| windows-oldrel | WARNING | 250 | ||
| wasm-release | OK | 168 |
Exports:col.keycombineKEGGnodescpd2keggcpdidmapcpdkegg2namecpdname2keggdownload.keggeg2idgeneannot.mapid2egkegg.species.codekeggview.graphkeggview.nativemol.sumnode.colornode.infonode.mappathviewreaction2edgesim.mol.datastrfitwordwrap
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64bitopsblobcachemclicpp11crayoncurlDBIfastmapgenericsgluegraphhttrIRangesjsonliteKEGGgraphKEGGRESTlifecyclememoisemimeopensslorg.Hs.eg.dbpkgconfigpngR6RCurlRgraphvizrlangRSQLiteS4VectorsSeqinfosysvctrsXMLXVector
Pathview: pathway based data integration and visualization
Last update: 2025-03-29
Started: 2013-11-01
