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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("NetPathMiner")
In most cases, you don't need to download the package archive at all.
NetPathMiner
NetPathMiner for Biological Network Construction, Path Mining and Visualization
Bioconductor version: 3.0
NetPathMiner is a general framework for network path mining using genome-scale networks. It constructs networks from KGML, SBML and BioPAX files, providing three network representations, metabolic, reaction and gene representations. NetPathMiner finds active paths and applies machine learning methods to summarize found paths for easy interpretation. It also provides static and interactive visualizations of networks and paths to aid manual investigation.
Author: Ahmed Mohamed <mohamed at kuicr.kyoto-u.ac.jp>, Tim Hancock <timothy.hancock at kuicr.kyoto-u.ac.jp>, Ichigaku Takigawa <takigawa at kuicr.kyoto-u.ac.jp>, Nicolas Wicker <nicolas.wicker at unistra.fr>
Maintainer: Ahmed Mohamed <mohamed at kuicr.kyoto-u.ac.jp>
Citation (from within R,
enter citation("NetPathMiner")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("NetPathMiner")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("NetPathMiner")
| R Script | NetPathMiner Vignette | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Classification, Clustering, GraphAndNetwork, Network, Pathways, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) |
| License | GPL (>= 2) |
| Depends | R (>= 3.0.2), igraph (>= 0.6) |
| Imports | |
| LinkingTo | |
| Suggests | rBiopaxParser(>= 2.1), RCurl, RCytoscape |
| SystemRequirements | libxml2, libSBML (>= 5.5) |
| Enhances | |
| URL | https://github.com/ahmohamed/NetPathMiner |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | NetPathMiner_1.2.0.tar.gz |
| Windows Binary | NetPathMiner_1.2.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | NetPathMiner_1.2.0.tgz |
| Mac OS X 10.9 (Mavericks) | NetPathMiner_1.2.0.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
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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