pathview
a tool set for pathway based data integration and visualization
Bioconductor version: 3.23 · Package version: 1.52.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pathview")Details
| Maintainer | Weijun Luo <luo_weijun@yahoo.com> |
| Author | Weijun Luo |
| License | GPL (>=3.0) |
| URL | https://github.com/datapplab/pathview, https://pathview.uncc.edu/ |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, Genetics, GraphAndNetwork, Metabolomics, Microarray, Pathways, Proteomics, RNASeq, Sequencing, Software, SystemsBiology, Visualization |
| Package Short Url | https://bioconductor.org/packages/pathview/ |
Citation
From within R, enter citation("pathview"):
Weijun Luo. pathview: a tool set for pathway based data integration and visualization. doi:10.18129/B9.bioc.pathview, R package version 1.52.0, https://bioconductor.org/packages/pathview.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | pathview_1.52.0.tar.gz |
| Windows binary (x86_64) | pathview_1.52.0.zip |
| macOS binary (arm64) | pathview_1.52.0.tgz |
| macOS binary (x86_64) | pathview_1.52.0.tgz |
Dependencies
Depends: R (>= 3.5.0)
Imports: KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, org.Hs.eg.db, KEGGREST, methods, utils
Suggests: gage, org.Mm.eg.db, RUnit, BiocGenerics
Reverse dependencies
Depends On Me (2): EGSEA, SBGNview
Imports Me (5): debrowser, EnrichmentBrowser, GDCRNATools, lilikoi, SQMtools
Suggests Me (5): CAGEWorkflow, gage, gageData, ReporterScore, TCGAbiolinks