DOI: 10.18129/B9.bioc.pcot2    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.13 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: 3.13

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")):


To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


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


PDF   Reference Manual


biocViews DifferentialExpression, GeneExpression, KEGG, Microarray, Network, Software
Version 1.60.0
In Bioconductor since BioC 1.9 (R-2.4) (15 years)
License GPL (>= 2)
Depends R (>= 2.0.0), grDevices, Biobase, amap
Suggests multtest, hu6800.db, KEGG.db, mvtnorm
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: