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clipper

Gene Set Analysis Exploiting Pathway Topology


Bioconductor version: Release (3.19)

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 (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("clipper")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("clipper")
clipper PDF R Script
Reference Manual PDF

Details

biocViews Software
Version 1.44.0
In Bioconductor since BioC 2.12 (R-3.0) (11 years)
License AGPL-3
Depends R (>= 2.15.0), Matrix, graph
Imports methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph, KEGGgraph, corpcor
System Requirements
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Suggests RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS, BiocStyle
Linking To
Enhances RCy3
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Package Archives

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

Source Package clipper_1.44.0.tar.gz
Windows Binary clipper_1.44.0.zip
macOS Binary (x86_64) clipper_1.44.0.tgz
macOS Binary (arm64) clipper_1.44.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/clipper
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/clipper
Bioc Package Browser https://code.bioconductor.org/browse/clipper/
Package Short Url https://bioconductor.org/packages/clipper/
Package Downloads Report Download Stats