pcot2

This package is for version 3.7 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see pcot2.

Principal Coordinates and Hotelling's T-Square method


Bioconductor version: 3.7

PCOT2 is a permutation-based method for investigating changes in the activity of multi-gene networks. It utilizes inter-gene correlation information to detect significant alterations in gene network activities. Currently it can be applied to two-sample comparisons.

Author: Sarah Song, Mik Black

Maintainer: Sarah Song <qson003 at stat.auckland.ac.nz>

Citation (from within R, enter citation("pcot2")):

Installation

To install this package, start R (version "3.5") and enter:


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

BiocManager::install("pcot2")

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("pcot2")
PCOT2 Vignette PDF R Script
Reference Manual PDF

Details

biocViews DifferentialExpression, GeneExpression, KEGG, Microarray, Network, Software
Version 1.48.0
In Bioconductor since BioC 1.9 (R-2.4) (17.5 years)
License GPL (>= 2)
Depends R (>= 2.0.0), grDevices, Biobase, amap
Imports
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Suggests multtest, hu6800.db, KEGG.db, mvtnorm
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Package Archives

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

Source Package pcot2_1.48.0.tar.gz
Windows Binary pcot2_1.48.0.zip
Mac OS X 10.11 (El Capitan) pcot2_1.48.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pcot2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pcot2
Package Short Url https://bioconductor.org/packages/pcot2/
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Old Source Packages for BioC 3.7 Source Archive