pathview
a tool set for pathway based data integration and visualization
Bioconductor version: Release (3.20)
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.
Author: Weijun Luo
Maintainer: Weijun Luo <luo_weijun at yahoo.com>
citation("pathview")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pathview")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("pathview")| Pathview: pathway based data integration and visualization | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, Genetics, GraphAndNetwork, Metabolomics, Microarray, Pathways, Proteomics, RNASeq, Sequencing, Software, SystemsBiology, Visualization |
| Version | 1.46.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (11.5 years) |
| License | GPL (>=3.0) |
| Depends | R (>= 3.5.0) |
| Imports | KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, org.Hs.eg.db, KEGGREST, methods, utils |
| System Requirements | |
| URL | https://github.com/datapplab/pathview https://pathview.uncc.edu/ |
See More
| Suggests | gage, org.Mm.eg.db, org.EcK12.eg.db, RUnit, BiocGenerics |
| Linking To | |
| Enhances | |
| Depends On Me | EGSEA, SBGNview |
| Imports Me | EnrichmentBrowser, GDCRNATools, MAGeCKFlute, debrowser, TCGAWorkflow, lilikoi, SQMtools |
| Suggests Me | TCGAbiolinks, gage, gageData, CAGEWorkflow, ReporterScore |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | pathview_1.46.0.tar.gz |
| Windows Binary (x86_64) | pathview_1.46.0.zip |
| macOS Binary (x86_64) | pathview_1.46.0.tgz |
| macOS Binary (arm64) | pathview_1.45.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/pathview |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/pathview |
| Bioc Package Browser | https://code.bioconductor.org/browse/pathview/ |
| Package Short Url | https://bioconductor.org/packages/pathview/ |
| Package Downloads Report | Download Stats |