GenomeStudio Plug-Ins
Overview of GenomeStudio Plug-Ins
The customized plug-ins, algorithms, and workflow solutions below can parse and analyze array data exported from GenomeStudio Software. These solutions are made available through Illumina Connect, a forum for sharing strategies to enhance Illumina BeadArray data analysis.
These tools are available for a broad range of genetic analysis applications, such as:- Whole-genome association
- Copy number variation analysis
- Gene expression analysis
- eQTL analysis
- Multi-assay data integration
- Biological pathway and network analysis
| Plug-in | Source | Functionality | BeadStudio Module Compatibility | GenomeStudio Module Compatibility | Plug-in Type/ Download |
|---|---|---|---|---|---|
| CGHFusion Plug-in | InfoQuant | Export of GenomeStudio GT data in CGHFusion |
N/A | v2010.3+ | Report / (ZIP) |
| ChromoZone | Illumina | Creates autobookmarks for single-sample analysis | GT v3.0+ | N/A | Autobookmarking / (ZIP) |
| CNVPartition v1.2.1 | Illumina | Estimates copy number and annotates regions with copy number variants (CNV) | GT v3.3.7+ | N/A | CNV / (ZIP) |
| CNVPartition v3.2.0 | Illumina | Estimates copy number and annotates regions with copy number variants (CNV) | N/A | GT v1.0+ |
CNV / (ZIP) |
| CNV Region Report |
Illumina | Generates i) A Standard Report that lists each copy number variation (CNV) and loss of heterozygosity (LOH) region for each sample; ii) An Allele-Specific Copy Number Report that reports copy number informed genotypes such as A- and ABB; iii) A PLINK CNV Input Report, which creates input files for some of the CNV features of the PLINK GWAS and CNV analysis application |
N/A | GT v1.0+ |
Report / (ZIP) |
| dChip InputReports | Illumina | Provides output data compatibility with dChip for CNV/LOH analysis | GT v3.1+ (you must also have dChip installed) | N/A | Report / (ZIP) |
| Exemplar | SapioSciences | Provides output data compatibility with Exemplar for whole genome association studies (WGAS) | GT v3.0+ | N/A | Report / (ZIP) |
| Haploview Input Report Plug-in v2.0.0 | Illumina | Export GT data for viewing in Haploview | N/A | GT v1.0+ | Report / (ZIP) |
| Helix Tree DSF | Golden Helix | Provides output data compatibility with HelixTree for WGAS | GT v3.0+ | N.A | Report / (ZIP) |
| Helix Tree DSF Report | Golden Helix | Export either genotype data or CNV data | GT v3.1+ | N/A | Report / (ZIP), (PDF Readme) |
| Golden Helix GenomeStudio DSF Plug-in | Golden Helix | Provides output compatibility with SVS 7 for SNP and CNV analysis | N/A | GT v1.0+ | Report / (ZIP) (Doc Readme) |
| LOH Detector | Illumina | Detects extended tracts of homozygosity. | GT v3.0+ | N/A | Autobookmarking / (ZIP) |
| LOH Score | Illumina | Estimates the likelihood of loss of heterozygostiy (LOH) in a region of interest. | GT v3.0+ | N/A | Column / (ZIP) |
| Merlin Input Report Plug-in v1.0.1 | Illumina | Used to create input files for the Merlin application | GT v3.2+ | N/A | Report / (ZIP) |
| Merlin Input Report Plug-in v2.0.1 | Illumina | Used to create input files for the Merlin application | N/A | GT v1.0+ | Report / (ZIP) |
| Nexus Copy Number Plug-in | BioDiscovery | Export BeadStudio CNV data to Nexus Copy Number | GT v3.1+ | N/A | Report / (ZIP) |
| Nexus Copy Number Plug-in | BioDiscovery | Export GenomeStudio CNV data to Nexus Copy Number | N/A | GT v1.0+ | Report / (ZIP) |
| Partek Copy Number Report Plug-in |
Partek | Export copy number analysis data for use in Partek's Genomic Suite |
N/A | GT v.1.0+ |
Report / (ZIP) |
| PennCNV | University of Pennsylvania | Automated analysis and visualization of CNV calls | GT v3.1+ via Universal CNV Adapter | GT v1.0+ via Universal CNV Adapter | CNV / (ZIP), (HTML Tutorial) |
| PLINK Input Report Plug-in | Illumina | Allows you to create input files for PLINK | N/A | GT v1.0+ | Report / (ZIP) |
| QuantiSNP | Oxford University | Automated analysis and visualization of CNV calls |
GT v3.1+ via Universal CNV Adapter | GT v1.0+ via Universal CNV Adapter | CNV / Contact: Ioannis Ragoussisor Cristopher Yau. |
| Universal CNV Adapter v1.0.4 | Illumina | Plug-in to QuantiSNP. For details, contact Illumina. | GT v3.1+ | N/A | CNV / (ZIP) |
| Universal CNV Adapter v2.0.2 | Illumina | Plug-in to QuantiSNP. For details, contact Illumina. | N/A | GT v1.0+ | CNV / (ZIP) |
| Plug-in | Source | Functionality | BeadStudio Module Compatibility | GenomeStudio Module Compatibility | Plug-in Type/ Download |
|---|---|---|---|---|---|
| IBD 2.1 GenomStudio plug-in | Integromics | Integromics Biomarker Discovery™ (IBD) for TIBCO Spotfire® Custom Output Report for GenomeStudio™ Gene Expression Module | N/A | GX v1.0+ | Report / (ZIP) |
| Illumina BeadStudio plugin for Nexus Expression | BioDiscovery | Export gene expression data for use in BioDiscovery's Nexus Expression | GT v3.1+ | N/A | Report / (ZIP) |
| Illumina GenomeStudio plugin for Nexus Expression | BioDiscovery | Export gene expression data for use in BioDiscovery's Nexus Expression | N/A | GX v1.0+ | Report / (ZIP) |
| ArrayExpress Data Submission Report v2.0.0 | Illumina | Export GX data in ArrayExpress format | N/A | GX v1.0+ | Report / (ZIP) |
| GEO Data Submission Report Plug-in v1.0.0 | Illumina | Export GX module data in GEO format | GX v3.2+ | N/A | Report / (ZIP) |
| GEO Data Submission Report Plug-in v2.0.0 | Illumina | Export GX module data in GEO format | N/A | GX v1.0+ | Report / (ZIP) |
| GX Custom Output Report Plug-in v1.0.0 | Illumina | Used to configure several report parameters including output columns and sample display | GX v3.3+ | N/A | Report / (ZIP) |
| GX Custom Output Report Plug-in v2.1.0 | Illumina | Used to configure several report parameters including output columns and sample display | N/A | GX v1.0+ | Report / (ZIP) |
| Partek Gene Expression Report Plug-in |
Partek | Export gene expression data for use in Partek's Genomic Suite |
N/A | GT v.1.0+ |
Report / (ZIP) |
| Plug-in | Source | Functionality | BeadStudio Module Compatibility | GenomeStudio Module Compatibility | Plug-in Type/ Download |
|---|---|---|---|---|---|
| Partek's Report Plug-In for GenomeStudio | Partek | Exports data into a project that Partek can directly open | N/A | GT v1.0+ | Report / (ZIP) |
| Methylation Custom Output Report Plug-in v2.0.0 | Illumina | Used to create input files for downstream applications | N/A | GT v1.0+ | Report / (ZIP) |