clipper

DOI: 10.18129/B9.bioc.clipper  

Gene Set Analysis Exploiting Pathway Topology

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

PDF	R Script	clipper
PDF		Reference Manual

Details

biocViews	Software
Version	1.38.0
In Bioconductor since	BioC 2.12 (R-3.0) (10 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	RCy3
URL
Depends On Me
Imports Me
Suggests Me	graphite
Links To Me
Build Report

Package Archives

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

Source Package	clipper_1.38.0.tar.gz
Windows Binary	clipper_1.38.0.zip
macOS Binary (x86_64)	clipper_1.38.0.tgz
macOS Binary (arm64)	clipper_1.38.0.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