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

clipper

Gene set analysis exploiting pathway topology

Bioconductor version: 2.13

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>

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	Software
Version	1.2.3
In Bioconductor since	BioC 2.12 (R-3.0)
License	AGPL-3
Depends	R (>= 2.15.0), Matrix, graph
Imports	methods, Biobase, igraph, gRbase (>= 1.6.6), qpgraph, KEGGgraph, corpcor, RBGL, Rcpp
Suggests	RUnit, BiocGenerics, RCytoscape(>= 1.6.3), graphite, ALL, hgu95av2.db
System Requirements
URL
Depends On Me
Imports Me
Suggests Me	graphite

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	clipper_1.2.3.tar.gz
Windows Binary	clipper_1.2.3.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	clipper_1.2.3.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats