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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("pathview")
In most cases, you don't need to download the package archive at all.
pathview
a tool set for pathway based data integration and visualization
Bioconductor version: 2.14
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 (from within R,
enter citation("pathview")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("pathview")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("pathview")
| R Script | Pathview: pathway based data integration and visualization | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, Genetics, GraphAndNetwork, Metabolomics, Microarray, Pathways, Proteomics, RNASeq, Sequencing, Software, SystemsBiology, Visualization |
| Version | 1.4.2 |
| In Bioconductor since | BioC 2.12 (R-3.0) |
| License | GPL (>=3.0) |
| Depends | R (>= 2.10), KEGGgraph, org.Hs.eg.db |
| Imports | Rgraphviz, graph, png, AnnotationDbi, KEGGREST, methods, utils |
| Suggests | gage, org.Mm.eg.db, RUnit, BiocGenerics |
| System Requirements | |
| URL | http://pathview.r-forge.r-project.org/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | clusterProfiler, gage, gageData |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | pathview_1.4.2.tar.gz |
| Windows Binary | pathview_1.4.2.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | pathview_1.4.2.tgz |
| Mac OS X 10.9 (Mavericks) | pathview_1.4.2.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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