In this section the core facility will add tools to facilitate and enhance analysis of Affymetrix microarray data. The tools are free to use and requires no registration. Installations and updates will be automatic, and require only the intitial installation of (see below).
For comments and questions, please contact David Brodin, david.brodin@biosci.ki.se.

Installing Java Runtime Environment (JRE)
To run the applications, you must have the Java Runtime Environment (JRE) version 1.2.2 or higher installed. JRE is free to use, and can be downloaded from:
http://java.com/java/download/index.jsp


AffyAnnotator
A tool for working with Affymetrix GeneChip expression data. Includes filtering of data, hyperlinks to bioinformatic resources, visualizations of expression data with focus on biological processes, molecular functions and cellular components (GO:s), and GenMap Pathways.
For further details, see the AffyAnnotator Manual.

Human Arrays:
Mouse Arrays:
 
Rat Arrays:
   
Yeast Arrays:
   

A test data set for the Focus array can be found here. Download the file, start 'HG-Focus' and click the 'Open Data' button in AffyAnnotator.


Requirements:
512M memory || at least 1024x800px screen resolution || JRE 1.5


Overlapper
A tool for checking overlap in lists of probe ID:s (or other items).


Requirements:
JRE 1.3


PeakAnnotator
A tool for annotating yeast chromosomal regions with genetic information.

 

Requirements:
JRE 1.3



TileWorker
A tool for annotating Human chromosomal regions with known genes.

 

Requirements:
JRE 1.5