Could somebody suggest free pathway visualization tool for omics data from plants?
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3.6 years ago
rimgubaev ▴ 270

I've tried to visualize my data using MapMan and KEGG Mapper but the quality of their pathway diagrams is much to be desired. I've also used BioCyc which is nice however today it requires a subscription.

Vizualization Pathways RNA-Seq • 2.9k views
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3.6 years ago

Have you tried Vanted ?

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Thanks, will try for sure!

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3.6 years ago
bigmawen ▴ 410

Pathview maps, integrates and renders a wide variety of biological data on relevant pathway graphs, and produce high quality graphics.
Pathview Web server:
https://pathview.uncc.edu/
Pathview R/Bioconductor package:
http://bioconductor.org/packages/release/bioc/html/pathview.html

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Nice one but there are only KEGG maps.

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10 months ago
bigmawen ▴ 410

The SBGNview package is the tool to work with pathway databases other than KEGG including Reactome, MetaCyc, SMPDB, PANTHER etc:
GitHub
https://github.com/datapplab/SBGNview
BioC
https://bioconductor.org/packages/SBGNview/

SBGNview is a tool set for pathway based data visualization, integration and analysis. SBGNview is similar and complementary to the widely used Pathview package, with the following key features:
• Pathway definition by the widely adopted Systems Biology Graphical Notation (SBGN);
• Supports multiple major pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP etc) and user defined pathways;
• Covers 5,200 reference pathways and over 3,000 species by default;
• Extensive graphics controls, including glyph and edge attributes, graph layout and sub-pathway highlight;
• SBGN pathway data manipulation, processing, extraction and analysis.

You may find an overview and quick start examples here:
https://github.com/datapplab/SBGNview
Main tutorial:
https://bioconductor.org/packages/release/bioc/vignettes/SBGNview/inst/doc/SBGNview.Vignette.html

Example visualization with Reactome pathway:
R-HSA-909733_Interferon alpha_beta signaling

Example visualization with PANTHER pathway:
enter image description here

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