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'))

Peer review:

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-1.45.0(bioc 3.20)pathview-1.44.0(bioc 3.19)

pathwaysgraphandnetworkvisualizationgenesetenrichmentdifferentialexpressiongeneexpressionmicroarrayrnaseqgeneticsmetabolomicsproteomicssystemsbiologysequencing

11.26 score 37 stars 13 packages 1.4k scripts 6.1k downloads 144 mentions 22 exports 45 dependencies

Last updated 23 days agofrom:87ffb7b842. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxWARNINGOct 30 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macWARNINGOct 31 2024

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

Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64bitopsblobcachemclicpp11crayoncurlDBIfastmapGenomeInfoDbGenomeInfoDbDatagluegraphhttrIRangesjsonliteKEGGgraphKEGGRESTlifecyclememoisemimeopensslorg.Hs.eg.dbpkgconfigplogrpngR6RCurlRgraphvizrlangRSQLiteS4VectorssysUCSC.utilsvctrsXMLXVectorzlibbioc

Pathview: pathway based data integration and visualization

Rendered frompathview.Rnwusingutils::Sweaveon Oct 30 2024.

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