To install this package, start R and enter:


In most cases, you don't need to download the package archive at all.


This is the development version of pcot2; for the stable release version, see pcot2.

Principal Coordinates and Hotelling's T-Square method

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

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




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



PDF R Script PCOT2 Vignette
PDF   Reference Manual


biocViews DifferentialExpression, Microarray, Software
Version 1.33.0
In Bioconductor since BioC 1.9 (R-2.4)
License GPL (>= 2)
Depends R (>= 2.0.0), grDevices, Biobase, amap
Suggests multtest, hu6800.db, KEGG.db, mvtnorm
System Requirements
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source pcot2_1.33.0.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) pcot2_1.33.0.tgz
Mac OS X 10.9 (Mavericks) pcot2_1.33.0.tgz
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center