clipper

Gene set analysis exploiting pathway topology

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("clipper")

Documentation

PDF R Script clipper
PDF   Reference Manual

Details

biocViews Software
Version 1.5.0
In Bioconductor since BioC 2.12 (R-3.0)
License AGPL-3
Depends R (>= 2.15.0), Matrix, graph
Imports methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph, KEGGgraph, corpcor, RBGL
Suggests RUnit, BiocGenerics, RCytoscape(>= 1.6.3), graphite, ALL, hgu95av2.db, MASS, BiocStyle
System Requirements
URL
Depends On Me
Imports Me
Suggests Me graphite

Package Downloads

Package Source clipper_1.5.0.tar.gz
Windows Binary clipper_1.5.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) clipper_1.5.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center