Package: pathview 1.47.0

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:Weijun Luo

pathview_1.47.0.tar.gz
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pathview.pdf |pathview.html✨
pathview/json (API)
NEWS

# 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-1.47.0(bioc 3.21)pathview-1.46.0(bioc 3.20)

pathwaysgraphandnetworkvisualizationgenesetenrichmentdifferentialexpressiongeneexpressionmicroarrayrnaseqgeneticsmetabolomicsproteomicssystemsbiologysequencing

11.25 score 40 stars 10 packages 1.6k scripts 6.3k downloads 144 mentions 22 exports 45 dependencies

Last updated 4 months agofrom:87ffb7b842. Checks:1 OK, 6 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 28 2025
R-4.5-winWARNINGJan 28 2025
R-4.5-linuxWARNINGJan 28 2025
R-4.4-winWARNINGJan 28 2025
R-4.4-macWARNINGJan 28 2025
R-4.3-winWARNINGJan 28 2025
R-4.3-macWARNINGJan 28 2025

Exports:col.keycombineKEGGnodescpd2keggcpdidmapcpdkegg2namecpdname2keggdownload.keggeg2idgeneannot.mapid2egkegg.species.codekeggview.graphkeggview.nativemol.sumnode.colornode.infonode.mappathviewreaction2edgesim.mol.datastrfitwordwrap

Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64bitopsblobcachemclicpp11crayoncurlDBIfastmapgenericsGenomeInfoDbGenomeInfoDbDatagluegraphhttrIRangesjsonliteKEGGgraphKEGGRESTlifecyclememoisemimeopensslorg.Hs.eg.dbpkgconfigplogrpngR6RCurlRgraphvizrlangRSQLiteS4VectorssysUCSC.utilsvctrsXMLXVector

Pathview: pathway based data integration and visualization

Rendered frompathview.Rnwusingutils::Sweaveon Jan 28 2025.

Last update: 2024-03-25
Started: 2013-11-01