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Software

Illumina

• GenomeStudio Genotyping Module
• GenomeStudio Gene Expression Module
• GenomeStudio Methylation Module
  

IlluminaConnect

• Algorithms, Plug-ins and third party Analysis Tools
  

Affymetrix

• Command Console® (AGCC) Software Download (zip, 166 MB)
• Data Transfer Tool (zip, 16.6 MB)
• Expression Console™ Software (zip, 40 MB)
• GeneChip® Operating Software (zip, 160 MB)
• GeneChip® Sequence Analysis Software (GSEQ) (zip, 13.6 MB)
• GeneChip® Targeted Genotyping Analysis Software (GTGS) (zip, 42.8 MB)
• Genotyping Console Software (zip, 100 MB)
• QC Toolbox Software, Version 2.2 (zip, 8.2 MB)
• Tiling Analysis Software (zip, 4.3 MB)
  

Sequenom

• MassARRAY Typer
  Software module for automated genotype calling, data storage and analysis.
  Includes tools for quantitative analysis
• MassARRAY QGE
  Software module for quantitative analysis of competitive PCR experiments
• MassARRAY EpiTYPER
  Software module for quantitative analysis of DNA methylation status
• MassARRAY OligoCheck
  Software module for automated quality control of oligonucleotides
• MassArray Assay Design
  Software module for designing of custom SNP genotyping assays.
  

Third Party Software

• Agilent Genespring GX Software
  Statistical Tools for Visulization and Analysis of Gene Expression Data
• Partek
  Integrated Genomics Analysis Tools including DGE and gene expression, RNA-seq and alternative splicing, copy number and association, ChIP-chip, ChIP-seq, and microRNA.
• PLINK
  PLINK is a free, open-source whole genome association analysis toolset.