 |
HelixTree | Feature List | Download |
Tutorials |
Support |
Golden Helix Inc
HelixTree, the flagship product of Golden Helix's SNP & 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 proven to be 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 new Genome-Wide Human SNP Array 5.0 and 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 easily take advantage of multi-core and multi-processor systems either locally or in a distributed grid environment using Condor® or the United Devices’ Grid MP™ platform. |
| |
|
|
| |
• |
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 over 100 peer reviewed publications. |
HelixTree was recently used extensively in the “first published study to utilize whole genome association technology in a psychiatric illness,” ¹ where psychiatric researchers analyzed Affymetrix 500K Mapping Array data and discovered a novel genetic risk locus associated with schizophrenia. Read Molecular Psychiatry Article
1 Quote from a press release (March 20, 2007) issued by the study's author, Dr. Todd Lencz.
GenSense | DataSheet | Support | Sales | GWA Toolkit
GenSense is an analysis and annotation software solution built on the InforSense Platform designed for analysing and annotating Genome Wide Association Studies.
GeneChip compatibility in GenSense allows direct importing of CHP and ARR files from both the SNP 5.0 and SNP 6.0 Genome-Wide Human SNP Arrays, together with the associated NetAffx information.
With the throughput that is possible from the new Affymetrix genotyping platforms, the promise of delivering novel biomarkers is more easily 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 GWAS in biological context. Features include:
| • |
Work with large volume data sets, including chips that measure up to one million SNP's across 1000's of samples |
| • |
Portal access for scientists and statisticians, which can be completely built and customized using workflows |
| • |
Automated quality control to filter SNP's and samples based on genotype quality score, genotype completion and sample duplication |
| • |
Statistical analysis of case control data and view the results with appropriate visualizations |
| • |
Filter, sort and prioritize SNPs |
| • |
Visualize case control test results as hit SNP's in a genome browser. |
| • |
Pre-built, flexible connectors for 3rd party tools (e.g. PHASE, PLINK and HaploView) and scripts (e.g. R and Perl) |
| • |
Link to phenotype data to find those SNPs most highly associated with disease and/or drug response |
| • |
Open SDK for developing and customizing analytics |
JMP Genetics |
Support |
Sales |
Home Page
JMP® Genetics, 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 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 as well as other sophisticated statistical tools, providing a single application for all 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, 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 & 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 Affymetrix 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 NetAffx, 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 tackles head-on 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 data quality control checks minimize loss of time in downstream analyses. Data 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 such as 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 to 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
The 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 proven itself and invaluable to discovery tool at leading pharmaceuticals and research institutes. Exemplar Analytics Features Include:
| |
• |
GeneChip Compatible™
- Wizard Driven import of CHP/CEL files with complete support of the new 5.0 and 6.0 arrays.
|
| |
• |
The Most Comprehensive Association Statistics
- Chi Square, OR, RR, Fishers Exact, Armitage Trend Test and more.
- Worlds Fastest Multiple Testing corrections: Permutation, FDR, Bonferroni.
- TDT and Haplotype Relative risk for Triad analysis.
|
| |
• |
Principal Component Analysis For Admixture Corrections
- Identifies and corrects for hidden sub-groups in GWAS studies.
|
| |
• |
Haplotype Analysis
- EM Algorithm inference of haplotype frequencies & 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.
- Published 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 SNP's to their related genes and ontological information with one click.
|
| |
• |
Whole Genome Viewer
- Layer 10K, 50K, 500K 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
- Architected to take advantage of today's dual and quad core processors to accelerate discoveries.
- Process thousands of samples of Affy 5.0 and 6.0 array data.
|
Exemplar Analytics can be evaluated with our free demonstration version upon request. For those needing assistance with data analysis, Sapio Consulting Services has 4 years experience conducting genome-wide association studies working with leading institutions including the NCI, NICHD, Cleveland Clinic and Children's Hospital of Philadelphia. For more information on our products or services, please email sales@sapiosciences.com or call 301-576-4155.
|
