Affymetrix - DevNet Tools



		DevNet Tools

The tools listed below are all unsupported 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 the associated 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 regarding these tools can be submitted to the Affymetrix forums. Whenever possible, documentation is also provided to help provide guidance on use of the tools. These are the only two methods of help that are provided for these tools.

		ANALYSIS TOOLS


		Affymetrix Power Tools (APT) - 10/5/2006 Download The Affymetrix Power Tools contains C++ source code for analyzing Affymetrix data and a set of command line tools built on this source code.

		seg-limo (SEGmented LInear MOdel) - 12/7/2006 Download seg-limo detects regions of differential expression from multiple transcription tiling array data sets at a user specified False Discovery Rate. It outputs the regions together with differential expression estimates in egr format for convenient visualization in the Integrated Genome Browser. It is written in ANSI C++ and has been tested on Intel Linux, both 32 and 64 bit. The source code is being distributed under the GPL license.

		Copy Number Pipeline - 3/30/2007 Download Copy Number Pipeline Binaries: Linux (32 bit and 64 bit), Windows, Mac (Fat binary: Intel & PPC), and Sparc Sun Solaris. (bz2, 15 MB) Download Library, parameter files, and SNP covariate files for Mapping 500K array. (b2, 69 MB) Download Library and SNP covariate files for Mapping 100K array. (b2, 21 MB) Download Library and SNP covariate files for Mapping 10K array. (b2, 5.7 MB) Download Example input data. (bz2, 755 MB) Download Example output data (created using example command lines included in the README). (bz2, 206 MB) Download Contains all of the above. (bz2, 1.1 GB) This is the command-line application for the Copy Number Pipeline which was developed for doing chromosome copy number and loss of heterozygosity analysis based on Affymetrix Mapping 500K arrays. This can also be used for the 100K and 10K arrays.

		Id_compare - 5/5/2006 Download \| Terms and Conditions ld_compare (version 1.0) is a tool for fast calculation of single-marker and multi-marker SNP correlations on a whole-genome scale. It is ideally suited for determination of genetic coverage for whole genome SNP panels and for generating raw SNP correlation data useful for selection of tag SNPs or evaluation of SNP tagging strategies.

		GCOS UTILITIES

		Sample/Experiment Object Importer Download \| Docs \| Terms and Conditions This application will import a text file into the GCOS system to create a sample and experiment. The application is written as a Windows service that monitors the activity of a user defined directory. Once a text file in the directory is detected the service will import the information from the file to create a GCOS sample and experiment.

		Template Export/Import Tool Download \| Docs Available in Download \| Terms and Conditions This tool provides the ability to transfer sample and experiment templates from one GCOS systems to another.

		AffyAnalyze Console Application Download \| Docs Available in Download \| Terms and Conditions The AffyAnalyze console application can be used to generate Affymetrix CHP files for any of the Expression, Mapping, Resequencing, and Universal chip types installed on a GCOS Client system.


		NETAFFX UTILITIES

		NetAffx Download Utility Download \| Docs \| Forum \| Terms and Conditions This utility provides a Windows operating system service to periodically query the NetAffx site and download user specified annotation files when updates are made available. Use the control panel applet that is installed with the software to configure the software. Commercial software providers are required to purchase a NetAffx Use License to bundle NetAffx content in their applications. Use of this software tool does not grant or substitute for this license.

		FILE MANIPULATION UTILITIES

		gtype_cel_to_pq Download \| Terms and Conditions The gtype_cel_to_pq tool extracts probesets from genotyping CEL filess into tab-delimited text suitable for import into other tools such as R.

		Tiling Utilities Download \| Terms and Conditions This is a collection of basic command-line utilities useful for working with tiling array data. They are all basic format conversion utilities for moving data between different formats related to tiling arrays, including tab-delimited text.

		CEL File Conversion Tool Download \| Forum \| Terms and Conditions The CEL File Conversion Tool converts all Affymetrix CEL files in a specified directory from version 3 format (ASCII - MAS 5 compatible format) to and from version 4 format (binary - GCOS compatible format).

		DAT File Viewer Download \| Forum \| Terms and Conditions The DAT File Viewer provides the ability to view a stand alone DAT file independent of any other file of data management system. The tool is used only to visualize a DAT file, no analysis is provided.

		Expression Intensity Exporter Download \| No Docs Available \| Terms and Conditions This tool will export the PM and MM intensities from an expression array to a text file.

		Mapping Intensity Exporter Download \| No Docs Available \| Terms and Conditions This tool will export the PM and MM intensities from a mapping array to a text file.

Affymetrix Tools
The Integrated Genome Browser and other tools are available in the Affymetrix Tools web page.