To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("clipper")

In most cases, you don't need to download the package archive at all.

clipper

 

Gene set analysis exploiting pathway topology

Bioconductor version: Release (3.1)

clipper is a package for topological gene set analysis. It implements a two-step empirical approach based on the exploitation of graph decomposition into a junction tree to 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:

source("http://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")

 

PDF R Script clipper
PDF   Reference Manual

Details

biocViews GeneExpression, GraphAndNetwork, KEGG, Pathways, Software
Version 1.8.0
In Bioconductor since BioC 2.12 (R-3.0) (2 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, RCytoscape(>= 1.6.3), graphite, ALL, hgu95av2.db, MASS, BiocStyle
SystemRequirements
Enhances
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_1.8.0.tar.gz
Windows Binary clipper_1.8.0.zip
Mac OS X 10.6 (Snow Leopard) clipper_1.8.0.tgz
Mac OS X 10.9 (Mavericks) clipper_1.8.0.tgz
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