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pathview (version 1.12.0)

a tool set for pathway based data integration and visualization

Description

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.

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Version

Version

1.12.0

License

GPL (>=3.0)

Maintainer

Weijun Luo

Last Published

February 15th, 2017

Functions in pathview (1.12.0)

eg2id

Mapping between different gene ID and annotation types
pathview-package

Pathway based data integration and visualization
sim.mol.data

Simulate molecular data for pathview experiment
mol.sum

Mapping and summation of molecular data onto standard IDs
combineKEGGnodes

Special treatment of nodes or edges for KEGG pathway rendering
node.info

Extract node information from KEGG pathway
download.kegg

Download KEGG pathway graphs and associated KGML data
demo.data

Data for demo purpose
kegg.species.code

Mapping species name to KEGG code
wordwrap

Wrap or break strings into lines of specified width
cpdidmap

Mapping between compound IDs and KEGG accessions
pathview

Pathway based data integration and visualization
node.color

Code molecular data as pseudo colors on the pathway graph
node.map

Map molecular data onto KEGG pathway nodes
korg

Mapping data on KEGG species code and corresponding Bioconductor gene annotation package
pathview-internal

Internal functions
cpd.accs

Mapping data between compound or gene IDs and KEGG accessions