ArrayStar v2.0 from DNASTAR®
ArrayStar | Support | Sales | DNASTAR | Download Trial

ArrayStar® is a desktop gene expression analysis software package designed to work with normalized Affymetrix GeneChip® expression data files. The easy-to-use software provides users with state-of-the-art visualization and statistical analysis tools that are useful in the monitoring of expression level changes throughout the researcher’s experiments and in recognizing co-regulation patterns. Clustering of data with both Heat Maps and k-Means methods can be performed. A wide range of filtering tools permits users to quickly explore numerous research options. Easily imported NetAffx™ gene annotations provide the latest annotation information for your research. The software is fully compatible with Windows Vista™ and XP. The software is sold with the same type of perpetual license that DNASTAR® has used to sell its sequence analysis software for 24 years. A no-charge, 30 day trial version of the software can be obtained by contacting DNASTAR at 608-258-7420 or going to their website at www.dnastar.com.

Biotique System's XRAY
Biotique | Support | Sales | Order

XRay is an affordable, powerful analysis tool for gene-level analysis of the new Human Gene ST 1.0 array as well as analysis of all exon level Affymetrix arrays. XRay is a Microsoft Excel plug-in allowing users to work in the comfortable environment of Microsoft Excel and leverage tight integration with Microsoft PowerPoint and Microsoft Work. A wizard-driven import engine allows new users to quickly enter data and automated analysis tracking autopopulates a Microsoft Word document allowing users complete documentation of their methods.

View a pre-recorded demonstration of data analysis from the Human Gene ST 1.0 array. (7 1/2 minutes)

Genedata's Expressionist®
Expressionist | Technical Specs | Demo | Support | Sales | Genedata

Genedata Expressionist® is a modular enterprise system for biomarker discovery. It represents a single-point-of-access for experimental, proprietary and public data, including sample information, raw and pre-processed transcriptomics, proteomics, metabolomics and lab chemistry data, analysis results, reports and documentation.

Expressionist's dedicated Refiner Array module performs automated quality assessment and pre-processing of Affymetrix GeneChip® Gene Expression data. Automated data pre-processing saves time, resources and cost in microarray analysis. Standardized workflows increase reproducibility and enable efficient, high-throughput processing of large experimental datasets. Comprehensive reporting and documentation features ensure effective project management and communication. Read more about Refiner Array.

The Genedata Expressionist® Analyst module features powerful algorithms and intuitive visualizers for efficient analysis of transcriptomics, proteomics, metabolomics and lab chemistry data. A flexible workflow system allows for standardized data analysis and convenient communication between bioinformaticians, computational biologists, statisticians and bench scientists. Finally, an open framework built on scalable enterprise architecture sets the basis for integration into any IT environment and extension with in-house algorithms, tools and databases. Read more about Analyst.

Genomatix's ChipInspector
ChipInspector | Technical Specs | Support | Sales | Genomatix

Microarray analysis and annotation software working with Affymetrix raw data files. ChipInspector carries out significance analysis on the single probe level. Probes with significant expression ratios are annotated based on the Genomatix proprietary genome annotation and analysis system ElDorado. Based on the annotation result, probes are assigned to transcripts. Graphical representations of the gene loci, featuring alternative transcripts as well as probe to transcript mapping, enable identification of differentially regulated transcripts, particularly when using Exon Arrays. Several clustering features allow to group probes with similar profiles. Results can easily be exported to Genomatix BiblioSphere PE for analysis of relations between expressed genes.

JMP® Microarray from SAS
JMP Microarray | Support | Sales | Home Page

JMP® Microarray, a desktop statistics tool for analyzing RNA expression, is an integrated environment for accessing, subsetting, analyzing, and exploring data patterns that can lead to the identification of promising new drugs. It uses JMP software as a powerful and dynamic data visualization and statistical analysis desktop client to SAS. Over 85 genomics processes employ JMP's Scripting Language (JSL) to launch open and customizable SAS macro programs in the background, enabling unparalleled data processing and statistical capabilities for rigorously understanding patterns and discoveries. JMP Microarray offers proven Design of Experiments (DOE) tools for creating efficient and unconfounded experiments; a wide range of input processes for popular genomic instrumentation; deep and broad statistical methods that optimize tradeoffs between sensitivity and specificity; and integrated links to many current bioinformatics annotation tools and websites.

Partek® Genomics Suite

Partek | Technical Specs | Support | Sales | Download | Partek Genomics Suite

Partek's Genomics Suite is an integrated statistical and visual analysis solution for GeneChip® experiments, optimized for fast and memory-efficient processing of large, ultra high-dimensional data. Proven, rigorously tested statistical methods are integrated with 2-D and 3-D interactive visualization allowing you to reliably explore, identify, and present important patterns in your data. All graphs can be exported in publication-quality vector graphic format. Multiple classification methods are integrated with gene selection for accurate diagnostic/prognostic prediction. Seamless integration with .CEL, .CDF, .CHP, and .EXP files includes fast, memory-efficient RMA and probe-level import. Partek GS automatically annotates all results and provides hyperlinks to NetAffx and other internet databases.

View a recent webcast from Partek illustrating methods to perform cancer classification and survival analysis.

Rosetta Biosoftware's Rosetta Resolver® System
Resolver System | Technical Specs | Support | Sales | Rosetta Biosoftware

The Rosetta Resolver system is a comprehensive gene expression analysis solution that incorporates powerful analysis tools with a robust, scalable database designed for pharmaceutical and biotechnology companies and research centers of excellence. The rigorous analysis methods, scalable database and extensive management tools of the Resolver system offer many opportunities for workflow and ad hoc-driven gene expression analyses. The Resolver system is an overall solution for gene expression analysis that is customizable and extendable to an organization’s informatics platform and to the unique research goals of its scientists.

Supports Analysis of 3' Gene Expression

This set of applications provides analysis solutions for Affymetrix 3'-based gene expression arrays, like the Human U133 Plus 2.0. Starting with data at either the probe (CEL file) or probe set level (CHP file), data summaries are generated and a variety of statistical methods are applied resulting in lists of differentially regulated genes. A variety of methods can be applied for data visualization. Genomic annotations are often intersected with expression data thus aiding the researcher in gaining biological insight from quantitative patterns of RNA levels within the cell.

Applied Maths' GeneMaths XT
GeneMaths XT | Technical Specs | Support | Sales | Applied Maths

GeneMaths XT is perhaps the most versatile software for microarray expression analysis available today. Its advanced concept of layers and subsets literally gives an extra dimension to expression analysis, by making it is possible to handle multiple data outputs, for example repeats, standard deviations, error values, etc., as well as multiple subsets of genes and/or arrays. The software uses full error handling through all analysis, mining, and statistics functions. Through its “Active History” concept, all steps of the analysis are recorded as scripts and can be repeated on other experiments. GeneMaths XT offers reliable normalization, interactive querying, pattern matching, time-course analysis, and a wide range of mining, clustering and classification techniques. A rich set of statistical tools, presented in well-documented wizards, allows even non-experts to perform reliable hypothesis testing. All functions are designed for data sets of any size and presented in an intuitive interface with powerful visualization tools. For the advanced user, GeneMaths XT is fully scriptable.

Register for a Free Trial of GeneMaths XT.

GenPlex™ from Istech
Istech | GenPlex™ | Support | Sales

GenPlex™ is an integrated software program for analyzing data from DNA microarray experiments using state-of-the-art statistical and mathematical algorithms. It provides powerful statistics, visualization and gene annotations in a user-friendly manner.

GenPlex™ performs various statistical analysis through five modules: Preprocessing, DEG Finding, Clustering, Classification, and Pathway Analysis. Two or multi-class analysis are possible using various parametric or non-parametric statistics in finding differential expressed genes. Genes showing similar expression patterns can be grouped using hierarchical, K-means and SOM algorithm. Discrimination of different classes is implemented using KNN, multi FLDA and other methods. Analysis is driven by a wizard style interface. Cross talk among different algorithms in different analysis modules provides users more stable and reliable results. GenPlex also supports biological annotation and automatic mapping of genes to pathways. The software provides all-in-one method solution which is whole computation where the user can easily obtain the best distinction error estimation.

Ocimum Biosolutions' Genowiz
Genowiz | Technical Specs | Support | Sales | Ocimum Biosolutions

Genowiz™ is a powerful gene expression analysis package for storing, processing and visualizing gene expression data efficiently. It includes a suite of advanced analysis methods and allows researchers to select analysis methods appropriate for their dataset. Genowiz™ supports the easy upload of both cDNA and Affymetrix data (.CDF, .CHP, .CEL) and annotates the data using NetAffx™ annotations and information from various databases. Support for probe level analysis algorithms like MAS 5.0 and RMA is provided. Genowiz™ allows researchers to update NetAffx™ annotations, thereby providing them the flexibility to view up-to-date annotations for genes. Genowiz™ has a wide range of statistical options for data normalization, transformation and filtration to provide a deeper and reliable insight into biological relevance of expression data. The application also comes equipped with several data analysis options like clustering, classification techniques, MIAME, Gene Ontology and pathways. Complete with excellent graphic visualization, it is an excellent tool for interpretation of biologically meaningful results. Genowiz™ is compatible with Windows, Linux and Mac operating systems.

Register for a Free Trial of Genowiz™.

OmicSoft's Array Studio
Trial Download | Features | Sales | Support | Home Page

Array Studio is a software package which provides state of the art statistics and visualization for the analysis of high dimensional quantification data (e.g. Microarray data) and genotype data (e.g SNP data). The software is designed for ease of use so that biologists can function at near the level of informatics specialists. Array Studio provides a fast, easy, and powerful solution for -omic data analysis.

Early versions of Array Studio have been used by over 200 industrial users in the past three years. More than 300 features in version 2.0 have been implemented based on feedback by those users.

Array Studio can be used for:

1. Affymetrix data QC, analysis and visualization (3’ IVT, exon or gene arrays, SNP arrays)
2. SNP/Genotyping analysis (Case/Control , Quantitative Trait , Categorical Trait , Stratified Trait, and Survival Trait Association Analysis)
3. GEO data importing, QC, analysis and visualization
4. General high dimensional data analysis, visualization, and manipulation
5. High dimensional data management
6. General data visualization and data manipulation

Spotfire's DecisionSite® for Functional Genomics
DecisionSite for Functional Genomics | Technical Specs | Support | Sales | Spotfire, Inc.

Spotfire DecisionSite® for Functional Genomics offers scientists a powerful visual analytic environment for exploring and finding unexpected relationships in gene expression and other types of genomic data. To better understand the large amounts of data from microarray experiments, rt-PCR and proteomic studies, DecisionSite for Functional Genomics provides rapid normalization, interactive filtering, clustering and statistical capabilities that give scientists deeper, more reliable insights into the biological relevance of the data. DecisionSite for Functional Genomics provides direct access to Affymetrix databases and chp files, NetAffx files and a number of other data sources.

View a pre-recorded product demonstration here.

VizX Labs' GeneSifter®
GeneSifter | Technical Specs | Support | Sales | VizX Labs

GeneSifter, the only microarray data analysis system optimized for biomedical research, won the 2005 “Best Practices Award for Product Innovation” in Bioinformatics in Drug Discovery from Frost & Sullivan. They noted that “the flexible nature of web-based GeneSifter enables scientists to better understand the biology behind their gene expression data,” and that scientists using GeneSifter products have testified to improved research, savings in training time, reduction in costs, and faster results. The GeneSifter product line includes GeneSifter Lab Edition, for individual researchers; GeneSifter Core Edition, for core facilities that prefer to administer their own accounts while taking advantage of GeneSifter's lower training and support costs; GeneSifter JumpStart, for scientists seeking to accelerate initial analysis efforts; the GeneSifter Data Center, an opportunity for any researcher to analyze high-quality, published data using the GeneSifter system for free; and MicroarraySuccess.com, for researchers new to microarrays. Free GeneSifter trial accounts are currently available.

View a pre-recorded product demo here.