Helix Tree | Feature List | Download | Tutorials | Support | Golden Helix Inc

HelixTree, the flagship product of Golden Helix’ SNP and Variation Suite, employs an unparalleled set of SNP analysis and genetic association tools offering more ways to uncover true genetic associations than any other programs. With citations in over 100 peer reviewed publications, HelixTree is recognized as the leading software application for targeted gene and whole-genome association studies.

Why HelixTree?

• GeneChip-compatible™: Directly import and analyze CHP files from Affymetrix GeneChip® Human Mapping Arrays, including the Genome-Wide Human SNP Array 5.0 and SNP Array 6.0.



• Comprehensive: Use an unparalleled set of tools for both population- and family-based association studies.
  • Streamline the import and management of large complex datasets with mixed variable types.
  • Calculate a host of summary statistics.
  • Assess and remedy data quality issues.
  • Conduct case/control, quantitative trait loci (QTL) and categorical-type analysis with numerous methods for allelic, genotypic, haplotypic, copy number variation, runs of homozygosity, multi-locus and regression-based association tests.
  • Detect genetic signals in the presence of confounding factors.
  • Control for false-positives.
  • Perform FBAT analysis and power calculations with an exclusively enhanced PBAT
  • Click here for a more complete feature list.


• Fast and Efficient: Fast algorithms and sparse data storage technology optimize computational speed and memory usage, enabling truly interactive whole-genome analysis with conventional computing hardware. Need more speed? Certain analyses can take advantage of multi-core and multi-processor systems either locally or in a distributed grid environment using Condor® or the Univa UD’s Grid MP.



• Easy to Use: A combination of intuitive wizards, superb data visualization tools, spreadsheets and scripting functions make HelixTree usable by both statistical geneticists and other life science experts.



• Extensible: A fully programmatic Python scripting interface enables automation of workflows, incorporation of user-defined statistical methods and integration with other packages. HelixTree is currently integrated with the R and S-Plus statistical packages.



• Proven: HelixTree has been cited in more than 100 peer-reviewed publications.

View a complete analysis workflow of data from the Affymetrix 500K Mapping Array Set.

GenSense | DataSheet | Support | Sales | GWA Toolkit

GenSense is an analysis and annotation software solution built on the InforSense Platform, designed for analyzing and annotating genome-wide association studies.

GeneChip® compatibility in GenSense allows direct importing of CHP and ARR files from the SNP Array 5.0 and SNP Array 6.0 together with the associated NetAffx® information.

With the throughput enabled by the new Affymetrix genotyping platforms, delivering novel biomarkers is within reach. Whole-genome association studies are becoming commonplace so analytic software needs to be highly flexible to enable the ad hoc integration of algorithms and data for placing genome-wide association studies in a biological context.

Features include:

• Work with large-volume data sets, including chips that measure up to 1 million SNPs across thousands of samples
• Portal access for scientists and statisticians, which can be completely built and customized using workflows
• Automated quality control to filter SNPs and samples based on genotype quality score, genotype completion and sample duplication
• Statistical analysis of case control data: view the results with appropriate visualizations
• Filter, sort and prioritize SNPs
• Visualize case control test results as hit SNPs in a genome browser.
• Pre-built, flexible connectors for third-party tools (e.g. PHASE, PLINK and HaploView) and scripts (e.g. R and Perl)
• Link to phenotype data to find SNPs most highly associated with disease and/or drug response
• Open SDK for developing and customizing analytics

JMP® Genomics | Support | Sales | Home Page

JMP Genomics, a desktop statistics tool for SNP analysis, is an integrated environment for accessing and analyzing Affymetrix SNP data. It uses JMP software as a powerful and dynamic data visualization and statistical analysis desktop client to SAS, and incorporates linkage disequilibrium analysis, whole-genome association analysis, and haplotype analysis using processes from SAS Genetics. In addition, loss of heterozygosity (LOH) and chromosomal copy number analyses can be performed on Affymetrix CNAT files using the partition tool in the JMP platform. The JMP for Genomics Suite also includes tools for proteomic and microarray analyses and other sophisticated statistical tools, providing a single application for all of your research needs.

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

Partek Genomics Suite (Partek GS) is an integrated statistical and visual analysis solution for GeneChip® experiments this is optimized for fast and memory-efficient processing of large, ultra high-dimensional data.

Partek GS supports single SNP association tests performed on allele, genotype and dominant/recessive models. Genotype data can be analyzed using statistical tests such as Chi², Hardy-Weinberg Equilibrium and linkage disequilibrium. Get accurate estimation of p-values in even the smallest datasets using Monte Carlo tests. Explore data with tabular analysis as well as visual analysis tools including frequency plots, biplots and heat maps, which can be used to visualize linkage disequilibrium within the data. In addition, after identifying loci of interest, explore copy number and LOH data in the same region. Gene and SNP lists can be easily created and exported. Corresponding data can be seamlessly linked to and visualized with the mapping array data.

Partek GS is GeneChip-compatible™, for gene expression, exon, chromosomal copy number, mapping and tiling array analysis and can seamlessly import data from a variety of file formats, while automatically providing links to the NetAffx® Analysis Center, UCSC Genome Browser, IGB and other internet databases.

Evaluate | Product Information | Sales | Support

Struggling to manage and analyze genotyping data from various sources instead of focusing on the science behind your study?

The Rosetta Syllego System addresses the informatics challenges associated with conducting genetic studies. Set your study apart by bringing all of your data and results together in one easy-to-access repository. Designed for biologists, statistical geneticists, and investigators responsible for generating genotyping data, the Syllego System enables you to:

• Align your scientific question with your genotyping technologies and data sources. Cleverly designed tools help you better plan and execute genetic studies across a variety of genotyping platforms and data sources.
• Generate high-quality data that does not cloud downstream analyses. User-defined statistical cuts and quality-control checks minimize loss of time in downstream analyses. Quality-Control results can be used to merge or refine relevant study data into analysis data sets targeted for further analysis.
• Use your analysis methods of choice. You can easily select and combine your relevant genotype and phenotype data to interface with the analysis environment of your choice, including PLINK and "R" and then easily visualize and share your results and methods.
• Maximize the return on your genetic study. The Syllego System gives you the tools to not only analyze your current study, but also catalog your study data and analysis results for use with public and privately available genotype data, future studies and collaboration efforts.

Put your genetic data management and analysis challenges behind you. Discover the Rosetta Syllego™ System.

Exemplar | Support | Sales | Sapio Sciences

Exemplar Analytics is the leading tool for performing genome-wide association studies with major publications in Nature Genetics. Exemplar has the most comprehensive set of analyses found in any product on the market and has proven itself an invaluable discovery tool at leading pharmaceuticals and research institutes. Features include:

• GeneChip-compatible™
• Wizard-driven import of CHP/CEL files with complete support of Affymetrix Genome-Wide Human SNP Arrays.
• The most comprehensive association statistics
  • Chi Square, OR, RR, Fishers Exact, Armitage Trend Test and more.
  • World’s fastest multiple testing corrections: Permutation, FDR and Bonferroni.
  • TDT and haplotype relative risk for triad analysis.
• Principal component analysis for admixture corrections
  • Identifies and corrects for hidden sub-groups in genome-wide association studies.
• Haplotype analysis
  • EM algorithm inference of haplotype frequencies and p-value of association.
  • Sliding window across whole genome.
• Copy number variation analysis
  • Finds insertions/deletions in the genome and graphically displays results.
  • Loss of heterozygosity analysis.
• Quantitative trait analysis
  • Predict traits from genetic and non-genetic factors.
  • ANOVA, linear and multiple regression.
• Multi-locus modeling
  • Uses advanced machine learning to discover multi-locus models that correspond with phenotypes.
  • Cited in landmark paper on AMD in Nature Genetics.
• Genetics database and annotations
  • Complete dBSNP, human gene and gene ontology database shipped with product.
  • Maps significant SNPs to their related genes and ontological information with one click.
• Whole-genome viewer
  • Layer 10K, 50K and 500K Array results on one view of the whole genome.
  • Mix and match different analyses in one view.
  • SNP-level annotations with related genes, positional info, etc.
• High performance, high scalability
  • Designed to take advantage of today’s dual- and quad-core processors to accelerate discoveries.
  • Process thousands of samples of data generated by the SNP Array 5.0 and SNP Array 6.0.

Exemplar Analytics can be evaluated with a free demonstration version upon request. For those needing assistance with data analysis, Sapio Consulting Services has four years of experience conducting genome-wide association studies with leading institutions including the NCI, NICHD, Cleveland Clinic and Children’s Hospital of Philadelphia. For more information on these products or services, please email sales@sapiosciences.com or call 301-576-4155.

BC/GENE | Solutions | Sales | Biocomputing Platforms

Biocomputing Platforms’ BC/GENE is a database environment designed to combine genotype data with phenotypes, maps and pedigrees and to create a productive statistical analysis pipeline. The platform has been designed to handle the output of modern high-throughput SNP genotyping technologies. BC/GENE enhances the use of the best genetic analysis programs by utilizing a web browser interface to set up analysis runs and generating input files automatically. BC/GENE also features a queue system for running multiple calculation tasks. Additional analysis tools and programs can be integrated into the system.

BC/SNPmax | Technical Specs | Support | Sales | Biocomputing Platforms

Biocomputing Platforms’ BC/SNPmax is a data management solution for whole-genome association studies. It integrates high-density SNP genotype data with phenotypes and maps, creating a highly productive data analysis pipeline with automated input file generation for analysis programs.

BC/SNPmax enhances the use of the best analysis programs for quality control, case/control analysis and family-based analysis. An advanced built-in queue system supports performing multiple, large parallel database transactions and calculation tasks. The queue system also makes it easier to build powerful calculation clusters.

A BC/SNPmax system can be implemented quickly, without requiring substantial resources for programming, allowing a research group’s programmers to focus on the top scientific priorities.

Progeny Lab | Technical Specs | Demo | Support | Sales | Progeny Software

Progeny Lab is a data management tool designed for large-scale genome-wide scans or specific target regions for linkage-type analysis or association studies. Comprehensive management includes:

• All variations of Affymetrix SNP sets (10K, 100K, 500K, etc.)
• High-speed imports of native Affymetrix CHP file genotypes or GDAS text outputs
• Automated error checking of genotype imports including Mendelian errors
• Custom exports to multiple analysis platforms
• Fully functional sample tracking
• Customizable database tracks both pedigrees and individuals, allowing unlimited custom data fields
• Functionality to manage all clinical and lab data in one relational database

View a recent GeneChip-compatible™ webcast illustrating how Progeny Lab can aid in data management from the GeneChip® Human Mapping 500K Array Set.

BioDiscovery | Support | Nexus Copy Number | Online Demo | Download Evaluation

Nexus Copy Number allows scientist to perform copy number analysis and visualization across large data sets that have thousands of samples and millions of probes per sample. The software supports many platforms including Affymetrix SNP array data. Nexus Copy Number provides an intuitive and interactive user interface that allows rapid identification of critical regions of genomic change in the entire population or sub-groups (e.g. different disease states). The publication-quality visualization tools are coupled with sophisticated statistical analysis for identification of areas of minimal overlap, statistically significant regions between two populations, clustering of samples based on genomic profiles, over representation of GO terms in regions of genomic instability, and much more. Nexus Copy Number is unlike any other tool for copy number analysis on the market due to BioDiscovery’s decade-long experience in developing pioneering software for the microarray market.

Sapio Sciences | Technical Specs | Support | Sales

Exemplar Copy Number Module is the first complete implementation of the copy number algorithm outside of the Copy Number Analysis Tool (CNAT). Exemplar has the following features:

• Highly scalable to the 500K Array.
• Full reference set generation capability (RefGen).
• Includes reference sets for 10K to 500K Arrays.
• High performance – five times faster on RefGen and two times faster on copy number analysis.
• Whole-Genome Viewer that can mix and match the following in one integrated view:
  • 10K, 50K, 100K, 250K and 500K Array results
  • Results from other Exemplar modules like statistical analyses
  • Loss of heterozygosity results
  • Imported results from third-party tools like CNAG, dChip, R, etc.
  • CNT import from CNAT
• Annotations of related genes, positional info from built-in, auto-updated genomics database
• Advanced filtering of results on value ranges or standard deviation from the mean
• Automatic, real-time gene ontology annotations

HelixTree | CNAM | Download | Webinars | Tutorials | Support | Golden Helix, Inc.

The Golden Helix’ Copy Number Analysis Module (CNAM) is an advanced software application which provides the high accuracy needed for whole genome copy number assocation studies.

CNAM provides a powerful set of novel methods and workflows for detecting copy number variations (CNVs) and performing association analysis on both CNV covariates and log ratios directly. It employs a proprietary optimal segmenting algorithm that can detect CNVs with astonishing accuracy. In fact, its unique multivariate method can detect CNVs at single marker resolution! You can also use CNAM to normalize log ratios against a reference set of your choice and correct for batch effects and stratification in your data using an Eigenstrat-based principal component analysis method.

Affymetrix Compatibility
CNAM substantially replicates the Affymetrix workflow for converting CEL files to log ratios. This includes:

• Quantile normalization (without gender bias)
• Virtual Array Generation (merging CN and SNP data, or NSP and STY)
• Normalizing log ratios against any reference population

This can be done for 500k, SNP 5.0, and SNP 6.0 arrays. Further, it is relatively high speed and works for thousands of samples. (2,000 samples can be processed overnight.) If preferred, CNAM can also read CNT and CNCHP files from Affymetrix's CNAT Batch Analysis and Genotyping Console Software 2.0 Software tools.

View a recent Affymetrix webcast from February 2008 for an overview of whole genome copy number (and SNP) association using Golden Helix software and Affymetrix arrays.

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

Partek 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. Statistical and visual features make it easy to detect regions of insertions and deletions on the genome. The Partek Genome Browser™ provides dot plots, box and whiskers, profiles and gene summaries to show the level of insertion/deletion and the number of affected individuals. All graphs can be exported in a publication-quality vector graphic format. Partek GS has seamless integration with CNAT version 3 output files and CEL files, and automatically associates annotations to all results, providing hyperlinks to the NetAffx® Analysis Center and other Internet databases.

View a recent Partek webinar from October 2007 that illustrates a complete workflow to identify regions of amplification and deletion using the Affymetrix copy number platform.

BLIS | Technical Specs | Support | Sales | Biotique Systems

The Biotique Local Integration System (BLIS) is an R&D enterprise integration solution that provides a web accessible environment for integrating, analyzing and sharing knowledge assets. BLIS brings together people, projects, disparate data sources and workflow applications. Furthermore, BLIS integrates biological data in the public domain with in-house proprietary (subscribed) databases, commercial and custom micro array designs, and NetAffx® annotations.

Designed for research executives, scientists and informatics experts alike, BLIS and its modules are licensed by more than 60 percent of large pharmaceutical corporations, more than 20 percent of small to medium-size pharmaceutical corporations, and two of the top 15 chemical companies.

GenomeQuest | Support | Sales | GenomeQuest

For the biologist who needs timely and comprehensive microarray annotation reports, GenomeQuest dramatically reduces the time spent searching databases and conducting sequence comparisons on entire lists of sequences. Its intuitive, easy-to-use software enables you to conduct your own searches, obtain best-fit answers to the search criteria you specify, and easily share your work with colleagues. GenomeQuest applies large-scale biological alignment methods to aid biological understanding based on the evolutionary linkage between two or more sequences. Built-in results analysis capabilities allow selection, sorting and filtering of huge data sets of alignments and annotations based on species, gene names, protein families and other scientific understanding linked to sequences and their annotations.

GenomeQuest integrates Affymetrix probe and target libraries for human, mouse and rat whole-genome array annotations with a worldwide network of transcript reference databases. Detailed reports are created automatically and can be published using Microsoft Office® or uploaded to popular microarray analysis packages. The system maintains continuous surveillance for new sequence information and sends email alerts to users when there is new information to discover. GenomeQuest is offered as a hosted ASP service or can be installed on customer servers providing security and integration with in-house data sets while requiring minimal administration. The system automatically updates itself with new sequence data from worldwide sequence repositories.

ElDorado | Technical Specs | Support | Sales | Genomatix

ElDorado is a genome annotation and analysis system with up-to-date annotations for more than 12 different organisms, comparative genomics (patent-pending) and the worlds largest quality-checked promoter annotation. Input sequences (mRNA/genomic) are mapped to all genomes in seconds including splice site predictions. Promoter sequences of regulated transcripts identified by ChipInspector can be extracted for further analysis. Effects of SNPs in promoter regions on transcription factor binding are annotated based on Genomatix’ MatInspector’s with its unique transcription factor binding site database. A direct link to Genomatix’ sophisticated gene regulation tools enables users to start sequence analysis right from the annotation.

GEMS Launcher | Technical Specs | Support | Sales | Genomatix

GEMS Launcher is a software and database package that analyzes gene regulatory mechanisms on the molecular level. GEMS Launcher includes more than 20 different software tools for promoter analysis, high-quality data on transcription factor binding sites (TFBS), promoter modules and a gateway to the worlds largest database of quality-assessed mammalian promoters. The tools detect common organization in promoters of transcripts identified by ChipInspector. They search the promoter database for these motifs to detect additional potentially co-regulated genes, thereby facilitating the design of target verification experiments. The tools using TFBS predictions are based on the gold-standard MatInspector which is included in the package.

Biotique | Support | Sales | Order

XRAY is the only available Excel add-in for expression that can rapidly normalize and analyze large numbers of (binary XDA format) CEL files. XRAY is also unique in that it simultaneously implements gene-level and exon (alternative splicing) studies, while simultaneously using all 6 million probes at every stage of analysis. All controls and results are in Excel so users should be familiar with the controls and worksheet project organization.

• Mixed-model ANOVA detects differential alternative splicing and gene expression even when data has dependencies.
• Project construction wizard and use of the familiar Excel interface that allows users to work immediately with little software product training.
• Runs on regular desktop and laptop computers (at least 700 MHZ with 500 MB RAM).
• Fixed-memory implementation means that practically unlimited numbers of CEL files can be analyzed simultaneously.
• Powerful enough to handle all the data on a chip with no filtering (but DABG and probe set annotation-level filters are available).
• The only system that simultaneously shows genomic, transcript cluster, probe-set, probe annotation and expression in a single view.
• Provides automatic annotation and links to public and NetAffx® databases.
• Validates statistical analysis.
• Efficient-quantile normalization and expression analysis for 20 CEL files runs in around 10 minutes on standard desktop computers (the application never requires more than 250MB RAM).

For more information or to contact sales directly, please call 775-787-9902 or email xray@biotiquesystems.com.

View a pre-recorded product demo on XRay v2.2, created in March 2007 (10 minutes)

View a recent GeneChip-compatible™ webcast illustrating analysis of the Human Exon Colon Cancer Data Set.

New XRAY demos for exon-expression analysis

View a two-minute demonstration of a typical workflow using Biotique’s XRAY for the analysis of GeneChip® Exon Arrays (2:12)

Windows Media Player | Quicktime

View a two-minute demonstration on the interpretation of GeneChip® Exon Array data from Biotique’s XRAY (2:30)

Windows Media Player | Quicktime

Expressionist | Technical Specs | Demo | Support | Sales | Genedata

Genedata’s Expressionist is a modular enterprise system for biomarker discovery. It represents a single-point-of-access system 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® Exon Array data. Automated data pre-processing saves time and resources in microarray analysis. Standardized workflows increase reproducibility and enable efficient, high-throughput processing of large experimental datasets. Performance benchmarks demonstrate nearly linear scalability when processing 50, 100, 500 or 1000 GeneChip Exon Arrays with Expressionist and nearly optimal parallelization of CPUs (tested up to 32 CPUs, e.g. exon chip processing – background subtraction, quantile normalization and RMA – takes 3.3 seconds with a 4 CPUs configuration!) 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.

ChipInspector | Technical Specs | Support | Sales | Genomatix

A microarray analysis and annotation software that works with Affymetrix raw data files. ChipInspector carries out significance analysis on the single-exon probe level. Exon 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, include the display of alternative transcripts as well as probe-to-exon mapping. Particularly when analyzing exon arrays, this allows identification of differentially regulated transcripts and potential new splice variants. Several clustering features allow the grouping of exon probes with similar profiles. Results can be easily be exported to Genomatix BiblioSphere PE for analysis of relations between expressed genes.

View a GeneChip-compatible™ webcast illustrating analysis of the Human Exon Colon Cancer Data Set.

JMP Genomics | Support | Sales | Home Page

JMP® Microarray, a desktop statistics tool for GeneChip® Exon Array analysis is an integrated environment for accessing discovering, analyzing, and exploring data patterns that can lead to key molecular insights (e.g. identification of biomarkers for promising new drugs). It uses JMP software as a powerful and dynamic data visualization and statistical analysis desktop client to SAS. Nearly 100 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 Genomics offers intuitive and proven design of experiments (DOE) tools for creating efficient and unconfounded experiments. After running the experiment, GeneChip Exon Array data can be uploaded from CEL files or txt files from Expression Console analysis can be directly imported using JMP Genomics’ utilities. Quality control and normalization can be performed with a variety of routines, and statistical modeling and significance testing can be performed using an efficient ANOVA for simple experimental designs, or mixed-model ANOVAs for more complex experimental designs and models. The latter are especially useful for detecting alternative splicing. In summary, JMP Genomics offers a wide range of input processes for popular genomic instrumentation; deep and broad statistical methods that optimize tradeoffs between sensitivity, specificity and reproducibility; and integrated links to many current bioinformatics annotation tools and websites including the NetAffx® Analysis Center, KEGG and Ingenuity.

View a pre-recorded product demonstration. (7 minutes)

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

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

Partek 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 2D and 3D interactive visualization allowing users to reliably explore, identify and present important patterns in their data. The Partek Genome Browser™ provides dot plots, box and whiskers, profiles, exon-level, gene-level and alternative splicing summaries. All graphs can be exported in a 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 GeneChip-compatible™ webcast that illustrates an analysis of the Human Exon Colon Cancer Data Set.

New Partek demo for exon expression analysis

View a brief demonstration of Partek Genomics Suite for the analysis of GeneChip® Exon Arrays.

Windows Media Player | Quicktime

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 monitoring expression-level changes throughout your 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. The software is fully compatible with Windows Vista™ and XP. It 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 visiting www.dnastar.com.

Biotique Systems | 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 you to work in the comfortable environment of Microsoft Excel and leverage tight integration with Microsoft PowerPoint and Microsoft Work. If you're a new user a wizard-driven import engine allows you to quickly enter data and automated analysis tracking autopopulates a Microsoft Word document allowing you complete documentation of your methods.

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

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

Genedata’s Expressionist® is a modular enterprise system for biomarker discovery. It represents a single-point-of-system 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 and resources 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.

ChipInspector | Technical Specs | Support | Sales | Genomatix

ChipInspector is a microarray analysis and annotation software that works 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 the grouping of probes with similar profiles. Results can be exported to Genomatix BiblioSphere PE for analysis of relations between expressed genes.

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. More than 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 | Technical Specs | Support | Sales | Download | Partek Genomics Suite

Partek 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 2D and 3D interactive visualization allowing users to reliably explore, identify and present important patterns in their data. All graphs can be exported in a 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® Analysis Center and other internet databases.

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

Rosetta 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 analysis. 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.

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 possible to handle multiple data outputs (e.g. 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 are 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.

Biotique Systems | 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 you to work in the comfortable environment of Microsoft Excel and leverage tight integration with Microsoft PowerPoint and Microsoft Work. If you're a new user a wizard-driven import engine allows you to quickly enter data and automated analysis tracking autopopulates a Microsoft Word document allowing you complete documentation of your methods.

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

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 analyses through five modules: Preprocessing, DEG Finding, Clustering, Classification, and Pathway Analysis. Two or multi-class analyses are possible using various parametric or non-parametric statistics in finding differentially expressed genes. Genes showing similar expression patterns can be grouped using hierarchical, K-means and SOM algorithms. 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 an all-in-one solution where the user can easily obtain the best distinction error estimation.

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 you to select analysis methods appropriate for your data set. Genowiz supports the upload of both cDNA and Affymetrix data (CDF, CHP and CEL files) 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 you to update NetAffx annotations, providing 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.

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

DecisionSite for Functional Genomics | Technical Specs | Support | Sales | Spotfire Inc.

Spotfire’s 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.