Pathview: an R/Bioconductor package for pathway-based data integration and visualization

By Weijun Luo, Cory R. Brouwer. Bioinform., 2013

2,066 citations recorded by the source corpus.

Summary: Pathview is a novel tool set for pathway-based data integration and visualization. It maps and renders user data on relevant pathway graphs. Users only need to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps and integrates user data onto the pathway and renders pathway graphs with the mapped data. Although built as a stand-alone program, Pathview may seamlessly integrate with pathway and functional analysis tools for large-scale and fully automated analysis pipelines. Availability: The package is freely available under the GPLv3 license through Bioconductor and R-Forge. It is available at http://bioconductor.org/packages/release/bioc/html/pathview.html and at http://Pathview.r-forge.r-project.org/. Contact: luo_weijun@yahoo.com Supplementary information: Supplementary data are available at Bioinformatics online.

Subfields: Cell Biology, Computer Vision and Pattern Recognition, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0c8dacf66498f7e73d73ceb508dd1d2af81b680e

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cell Biology

1. E. Ulgen
2. Osman Ugur Sezerman
3. Ozan Ozisik

In Computer Vision and Pattern Recognition

1. E. Ulgen
2. Osman Ugur Sezerman
3. Ozan Ozisik

In Molecular Biology

1. E. Ulgen
2. Osman Ugur Sezerman
3. Ozan Ozisik
4. Weijun Luo
5. Cory R. Brouwer

Citations in the corpus

• BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine (2016, methodology): “The function of targets’ pathway mapping was implemented based on Pathview 54 , which is an R package for pathway-based data integration and visualization.”
• Pathview Web: user friendly pathway visualization and data integration (2017, methodology): “These tools have been extensively reviewed and compared in recent literature (10,16,17).”
• pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks (2019, methodology): “The KEGG pathway diagrams are created using the R package pathview (Luo and Brouwer, 2013).”