a tool set for pathway based data integration and visualization


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Documentation for package ‘pathview’ version 1.48.0

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pathview-package Pathway based data integration and visualization
bods Mapping data on KEGG species code and corresponding Bioconductor gene annotation package
col.key Code molecular data as pseudo colors on the pathway graph
combineKEGGnodes Special treatment of nodes or edges for KEGG pathway rendering
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
cpd2kegg Mapping between compound IDs and KEGG accessions
cpdidmap Mapping between compound IDs and KEGG accessions
cpdkegg2name Mapping between compound IDs and KEGG accessions
cpdname2kegg Mapping between compound IDs and KEGG accessions
demo.paths Data for demo purpose
download.kegg Download KEGG pathway graphs and associated KGML data
eg2id Mapping between different gene ID and annotation types
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
geneannot.map Mapping between different gene ID and annotation types
gse16873.d Data for demo purpose
id2eg Mapping between different gene ID and annotation types
kegg.met Mapping data between compound or gene IDs and KEGG accessions
kegg.species.code Mapping species name to KEGG code
keggview.graph Pathway based data integration and visualization
keggview.native Pathway based data integration and visualization
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
mol.sum Mapping and summation of molecular data onto standard IDs
node.color Code molecular data as pseudo colors on the pathway graph
node.info Extract node information from KEGG pathway
node.map Map molecular data onto KEGG pathway nodes
paths.hsa Data for demo purpose
pathview Pathway based data integration and visualization
reaction2edge Special treatment of nodes or edges for KEGG pathway rendering
rn.list Mapping data between compound or gene IDs and KEGG accessions
sim.mol.data Simulate molecular data for pathview experiment
strfit Wrap or break strings into lines of specified width
wordwrap Wrap or break strings into lines of specified width