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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("clipper")
In most cases, you don't need to download the package archive at all.
clipper
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see clipper.
Gene Set Analysis Exploiting Pathway Topology
Bioconductor version: 3.4
Implements topological gene set analysis using a two-step empirical approach. It exploits graph decomposition theory to create a junction tree and reconstruct the most relevant signal path. In the first step clipper selects significant pathways according to statistical tests on the means and the concentration matrices of the graphs derived from pathway topologies. Then, it "clips" the whole pathway identifying the signal paths having the greatest association with a specific phenotype.
Author: Paolo Martini <paolo.cavei at gmail.com>, Gabriele Sales <gabriele.sales at unipd.it>, Chiara Romualdi <chiara.romualdi at unipd.it>
Maintainer: Paolo Martini <paolo.cavei at gmail.com>
Citation (from within R,
enter citation("clipper")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("clipper")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("clipper")
| R Script | clipper | |
| Reference Manual |
Details
| biocViews | Software |
| Version | 1.14.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (4 years) |
| License | AGPL-3 |
| Depends | R (>= 2.15.0), Matrix, graph |
| Imports | methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph, KEGGgraph, corpcor, RBGL |
| LinkingTo | |
| Suggests | RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS, BiocStyle |
| SystemRequirements | |
| Enhances | RCytoscape(>= 1.6.3) |
| URL | |
| Depends On Me | |
| Imports Me | ToPASeq |
| Suggests Me | graphite |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | clipper_1.14.0.tar.gz |
| Windows Binary | clipper_1.14.0.zip |
| Mac OS X 10.9 (Mavericks) | clipper_1.14.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/clipper/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/clipper/ |
| Package Downloads Report | Download Stats |
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