The tools listed below are all tools that have been developed internally at Affymetrix. They are not validated products and are provided as is and without warranty. Use of these tools is offered to those customers who understand and accept these terms and conditions and wish to take advantage of their potential to help manage and analyze GeneChip® data. If any of these tools are to be used in a production environment it is the responsibility of the end-user to perform the required validation.
Comments on the tools can be submitted to the upcoming Affymetrix forums. Whenever possible, documentation is provided to provide guidance on use of the tools. These are the only two methods of help that are provided for these tools.
Expression Console™ Software
Affymetrix® Expression Console software supports Probe Set summarization and CHP file generation for both 3' Expression (e.g. GeneChip® Human Genome U133 Plus 2.0 Array) and Exon Arrays (e.g. GeneChip® Human Exon 1.0 ST Array). The Expression Console workflow provides the user with a choice of the more commonly used Probe Set summarization algorithms.
Transcriptome Analysis Console Software
Transcriptome Analysis Console (TAC) Software, developed by Affymetrix, enables the identification of differentially expressed genes and exons and the visualization of alternative splicing events for determining possible transcript isoforms that may exist in your specific samples. TAC Software supports most Affymetrix® gene expression arrays.
Genotyping Console™ Software
Affymetrix® Genotyping Console is a new genotyping analysis software package designed to streamline whole-genome genotyping analysis and quality control for the Genome-Wide SNP Arrays 5.0 and 6.0. Genotyping Console's QC and visualization tools easily identify and segregate sample outliers. SNP cluster visualization provides a detailed look at the performance of SNPs of interest. Reporting of seventy-two signature SNPs enable verification of a sample's identity if compared to known genotypes for that sample. In addition, flexible SNP filtering, data management and visualization export features make it easy to share data with collaborators and downstream application software.
Axiom® CNV Summary Tools Software, Version 1.0
Affymetrix' Axiom® CNV Summary Tools enable copy number analysis on data from Axiom® Genotyping Arrays by calculating log2 ratios and B allele frequencies from Axiom genotyping data. Also included in the Axiom CNV Summary Tools Software package is Affymetrix® CNV Viewer, which allows straightforward visualization of copy number changes across the genome with the ability to zoom in for inspection down to single markers. For a more comprehensive analysis, the software exports files compatible for use with BioDiscovery Nexus Copy Number Software and PennCNV Software.
Tiling Analysis Software (TAS)
The TAS software provides analysis capabilities specifically for the GeneChip® Tiling Arrays. TAS analyzes feature intensity data stored in GCOS output .CEL files and produces:
- Signal and p-values for each genomic position interrogated.
- Computation of genomic intervals based on computed signal and p-values
- Computation of summary statistics
- Visualizations for assessing the quality of the array data
Integrated Genome Browser
The Integrated Genome Browser (IGB, pronounced ig-bee) is an application intended for visualization and exploration of genomes and corresponding annotations from multiple data sources.
Source code for IGB is released under the Common Public License, v1.0, an OSI approved open source license. IGB uses other open source software packages that are distributed in binary form with the IGB source code release, including Xerces from Apache, and Jetty from Mortbay Consulting, which are covered by their own open source licenses. IGB is Copyright (c) 2000-2006 Affymetrix, Inc. Research and development of IGB is supported in part by NIH grant R01HG003040.
Library File Installer Upgrade
The Library File Installer Upgrade is an application to update the CustomExpress™ Arrays expression library files to the latest version. This latest version is required to perform a fresh install of the CustomExpress Arrays expression library files on a GCOS v1.4 Server based on Oracle 10g.
This tool requires Java to be installed. Please go to the Java website and download the appropriate Java Runtime Environment.
For more information on installation and a quick start guide, please refer to the Install Guide.
File manipulation and other developer tools are available in the DevNet Tools web page.