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Ariadne Genomics
9430 Key West Avenue
Rockville, MD 20850
Phone: 240.453.6272
Contact: David Denny
Email: ddenny@ariadnegenomics.com
Web: www.ariadnegenomics.com
Application Area Supported: Gene Expression (GEX)
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BioBase
BIOBASE GmbH Halchtersche Strasse 33
D-38304 Wolfenbuettel/Germany
Phone: +49 5331 8584 0
Contact: Frank Schacherer
Email: Frank.Schacherer@biobase-international.com
Web: www.biobase-international.com
Application Area Supported: Gene Expression Analysis
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BioComputing Platforms Ltd.
Innopoli 2
Tekniikantie 14
02150 Espoo
Finland
Phone: +358-40-5780587
Contact: Anni Ahonen-Bishopp
Email: anni.ahonen-bishopp@bcplatforms.com
Web: www.bcplatforms.com
Application Area Supported: Genotyping (GT)
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BioDiscovery
2121 Rosecrans Ave., Suite 3315
El Segundo, CA 90245
Phone: 310.414.8100
Contact: Dr Soheil Shams
Email: sshams@biodiscovery.com
Web: www.biodiscovery.com
Application Areas supported: Genotyping (GT), Copy Number (CN) analysis
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BioTeam, Inc.
7 Derosier Drive
Middleton, MA 01949
Phone: 877.246.2992 x101
Contact: Stan Gloss
Email: stan@bioteam.net
Web: www.bioteam.net/specialty/nextGenSeq.html
Application Areas supported: WIKI-LIMS for Sequencing applications
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CLC bio
Gustav Wieds Vej 10
8000 Aarhus C
Denmark
Contact: Thomas Knudsen
Email: tknudsen@clcbio.com
Web: http://www.clcbio.com/ngs
Application Area Supported: Sequencing Solutions
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DNASTAR Inc.
3801 Regent Street
Madison, WI 53705 USA
Phone: 608.258.7420
Contact: Bob Steinhauser
Email: steinhauserb@dnastar.com
Web: http://www.dnastar.com
Application Areas supported: Gene Expression & Sequencing
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Genedata AG
Maulbeerstrasse 46
CH-4016 Basel, Switzerland
Phone: +41 61 697 5115
Contact: Patrick Wieghardt
Email: expressionist@genedata.com
Web: www.genedata.com
Application Area Supported: Gene Expression (GEX)
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GeneGo
169 Saxony Rd, Suite 109
Encinitas, CA 92024
Phone: 858.756.7996
Contact: Julie Bryant
Email: julie@genego.com
Web: www.genego.com/metacore.php
Application Area Supported: Pathway Analysis & Gene Expression
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GenoLogics Life Sciences Software
4464 Markham Street, Suite 2302
Victoria, BC, Canada, V8Z 7X8
Phone: 1.866.457.5467, 1.250.483.7011
Contact: Laurie Phillips
Email: laurie.phillips@genologics.com
Web: www.genologics.com
Application Areas Supported: Genotyping (GT), Gene Expression (GEX)
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GenomeQuest
1700 West Park Drive, Suite 260
Westborough, MA 01581
Phone: 508.616.0100 x121
Contact: Anthony Salerno
Email: anthony.salerno@genomequest.com
Web: www.genomequest.com
Application Areas Supported: Sequencing applications
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Geospiza, Inc.
100 West Harrison
Seattle, WA 98119
Phone: 206.633.4415
Contact: Laura Lucas
Contact phone: 206.633.4403 x 119
Email: laural@geospiza.com
Web: http://www.geospiza.com
Application Area Supported: Whole-Genome SNP Analysis, Copy Number Variation (CNV) Analysis, Gene Expression Analysis, Sequencing Application
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Golden Helix, Inc.
716 S. 20th Ave., Suite 102
Bozeman, MT 59718
Phone: 406.585.8137
Contact: Josh L. Forsythe
Email: jlforsythe@goldenhelix.com
Web: www.goldenhelix.com
Application Area Supported: Genotyping (GT), Copy Number (CN) analysis
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infoQuant
Suite 326
8 Shepherd Market
London W1J 7JY, UK
Phone: 617.475.5167
Contact: Anton Petrov
Email: info@infoquant.com
Web: www.infoquant.com
Application Area Supported: Copy Number (CN) analysis
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InforSense, LLC
155 Second Street
Cambridge, MA 02141
Phone: +44 20 8237 8453
Contact: Robin Munro
Email: rmunro@inforsense.com
Web: www.inforsense.com
Application Area Supported: Genotyping (GT)
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Ingenuity Systems, Inc.
1700 Seaport Blvd. Suite 300
Redwood City, CA 94063
Phone: 650.381.5150
Contact: Heidi Bullock
Email: hbullock@ingenuity.com
Web: www.ingenuity.com
Application Area Supported: Gene Expression (GEX)
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Partek Incorporated
12747 Olive Blvd., Suite 205
St. Louis, Missouri 63141
Phone: 314.878.2329
Contact: Shirley Gross
Email: sgross@partek.com
Web: www.partek.com
Application Areas Supported: Genotyping (GT), Gene Expression (GEX), Copy Number Variation Analysis (CNV)
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Progeny Software, LLC
130 S. Main Street, Suite 120
South Bend, IN 46601
Phone: 800.776.4369
Contact: Andrew Brown, Ph.D.
Email: abrown@progenygenetics.com
Web: www.progenygenetics.com
Application Area Supported: Genotyping (GT)
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Rosetta BioSoftware
401 Terry Ave. N.
Seattle, WA 98109
Phone: 206.926.1200
Contact: Sasha Paegle
Email: Sasha_Paegle@rosettabio.com
Web: Visit Resolver site
Web: Visit Syllego site
Application Areas Supported: Genotyping (GT), Gene Expression (GEX)
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Sapio Sciences, LLC
2391 Mayfield Street, Suite 201
York, PA 17402
Phone: 301.576.2729
Contact: Dr Kevin Cramer
Email: kcramer@sapiosciences.com
Web: www.sapiosciences.com
Application Areas Supported: Copy Number (CN) analysis, Genotyping (GT)
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SAS Institute Inc.
SAS Campus Drive
Cary, North Carolina 27513
Phone: 919.677.8008
Contact: Doug Robinson, Ph.D.
Email: Doug.Robinson@jmp.com
Web: www.jmp.com
Application Areas Supported: Genotyping (GT), Gene Expression (GEX)
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Stratagene, Inc.
11011 N. Torrey Pines Road
La Jolla, CA 92037
Phone: 858.373.6300
Contact: Dr David Edwards
Email: david.edwards@stratagene.com
Web: www.stratagene.com
Application Areas Supported: Copy Number (CN) analysis, Gene Expression (GEX)
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VizX Labs/GeneSifter
Queen Anne Square
200 West Mercer St., Suite 500
Seattle, WA 98119-3995
Phone: 877.932.4363
Contact: Jeff Kozlowski
Email: jeff@genesifter.net
Web: www.genesifter.net
Application Area Supported: Gene Expression (GEX)
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University of Pennsylvania
Department of Genetics
University of Pennsylvania
Philadelphia, PA 19104
Phone: 215.898.0021
Contact: Kai Wang
Email: kai@mail.med.upenn.edu
Web: www.neurogenome.org/cnv/penncnv/
Application Areas Supported: Copy Number Variation Analysis (CNV)
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The Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford
OX3 7BN
United Kingdom
Phone: +44 (0)1865 287500
Contact: Iaonnis Ragoussis
Email: ioannisr@well.ox.ac.uk
Web: www.well.ox.ac.uk
Application Area Supported: Copy Number Variation (CNV) analysis
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plink...
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PLINK
Whole genome association analysis toolset
The link below describes how Illumina’s WG arrays data from BeadStudio can
be converted into a file input format for WGAS using PLINK.
PLINK
Support for BeadStudio data output
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dChip
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dChip
Analysis and visualization of gene expression and SNP microarrays
Contact: Dr Cheng Li
Department of Biostatistics, Harvard School of Public Health and
Department of Biostatistics and Computational Biology
Dana-Farber Cancer Institute
375 Longwood Ave, 6th Floor
Boston, MA, 02215
Email: cli@hsph.harvard.edu
Web: http://biosun1.harvard.edu/complab/dchip/
Application Areas Supported: Copy Number Variation (CNV) analysis, Gene Expression (GEX)
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LUMI
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LUMI
An integrated solution for Illumina microarray data analysis, available as an R/Bioconductor application.
Contact: Dr Simon Lin
Robert H. Lurie Comprehensive Cancer Center
676 N Saint Clair, Suite 1200
Northwestern University
Chicago, IL 60611
Email: S-Lin2@northwestern.edu
Web: http://www.bioconductor.org/packages/2.0/bioc/html/lumi.html
Application Area Supported: Gene Expression (GEX)
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 CNV Analysis Plug-ins
|
| Download |
Name |
Type |
Source |
Functionality |
BeadStudio Module Compatibility |
*.zip file
 |
cnvPartition v1.0.2 |
Algorithm |
Illumina |
Estimates copy number and annotates regions with copy number variants (CNV) |
GT Module v3.1 |
*.zip file
|
ChromoZone |
Autobook- marking |
Illumina |
Creates autobookmarks for single-sample analysis |
GT Module v3.0 and higher |
*.zip file
|
dChip InputReports |
Report |
Illumina |
Provides output data compatibility with dChip for CNV/LOH analysis |
GT Module v3.1
You must also have dChip installed |
*.zip file
Read Me |
Helix Tree Dsf Report |
Report |
Golden Helix |
Export either
genotype data or CNV data |
GT Module v3.1 |
*.zip file
|
Nexus CGH Plug-in for CNV Analysis |
Report |
BioDiscovery |
Export Illumina CNV data to Nexus CGH |
GT Module v3.1 |
*.zip file
|
Partek GS custom report for CNV analysis |
Report |
Partek |
Export genotyping or CNV data to Partek GS |
BeadStudio Module Compatibility GT Module v 3.1 or higher |
*.zip file
Tutorial |
PennCNV |
Algorithm |
U of Pennsylvania |
Automated analysis and visualization of CNV calls |
BeadStudio GT v3.1 and higher |
| Contact: Ioannis Ragoussis or Christopher Yau. |
QuantiSNP |
Algorithm |
Oxford U |
For details, contact Ioannis Ragoussis or Christopher Yau |
GT Module v3.1 |
*.zip file
|
Universal CNVAdapter
(compatible with QuantiSNP) |
Column |
Illumina |
Plug-in to QuantiSNP. For details, contact Illumina. |
GT Module v3.1 |
|
Learn more about analyzing CNV with Illumina BeadStudio plug-ins.
|
 |
Custom Report Plug-ins
|
| Download |
Name |
Type |
Source |
Functionality |
BeadStudio Module Compatibility |
*.zip file
|
CGHFusion Plugin |
Report |
InfoQuant |
Export of BeadStudio GT data into CGHFusion |
BeadStudio GT v3.2 and higher |
*.zip file
|
ArrayAssist Explorer v1 from Strand |
Column |
Stratagene / Agilent |
Provides output data from BeadStudio to ArrayAssist |
GT Module v3.0 and higher |
*.zip file
|
Exemplar |
Report |
Sapio Sciences |
Provides output data compatibility with Exemplar for whole genome association studies (WGAS) |
GT Module v3.0 and higher |
*.zip file
|
HelixTree DSF |
Report |
Golden Helix |
Provides output data compatibility with HelixTree for WGAS |
GT Module v3.0 and higher |
*.zip file
|
GX Custom Output Report |
Report |
Illumina |
Used to configure several report parameters including output columns and sample display |
BeadStudio GX v3.3 and higher |
*.zip file
|
Merlin Input Report |
Report |
Illumina |
Used to create input files for the Merlin application |
BeadStudio GT v3.2 and higher |
 |
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