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Welcome

This source code repository contains data anaysis code and data files developed for CressExpress 2.0, an on-line tool for co-expression analysis. The on-line tool is implemented (mostly) in Java. This repository contains R code we used to prototype analyses, check integrity of data, and document co-expression analysis focused on specific genes or pathways.

CressExpress 2.0 (as of Sept 2014) is still being developed and is not yet publicly avaiable. However, CressExpress Classic is available from CressExpress.org.

About folders in this repository

Folders contained in this repository represent data analysis "modules" that are mostly independent unites but sometimes use files and results from other modules.

SomeAgainstAll

This module shows how to compare a set of query genes (probesets) to all other genes (probe sets) on an array. Arrays are from the ATH1 platform and data are from the Gene Expression Omnibus.

ExternalDataSets

Contains data files downloaded from other Web sites or generated in upstream bioinformatics data processing steps.