clipper
Gene Set Analysis Exploiting Pathway Topology
Bioconductor version: Release (3.20)
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("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 | R Script | |
| Reference Manual |
Details
| biocViews | Software |
| Version | 1.46.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (11.5 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 | |
| URL |
See More
| Suggests | RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS, BiocStyle |
| Linking To | |
| Enhances | RCy3 |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | clipper_1.46.0.tar.gz |
| Windows Binary (x86_64) | clipper_1.46.0.zip |
| macOS Binary (x86_64) | clipper_1.46.0.tgz |
| macOS Binary (arm64) | clipper_1.46.0.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 |