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Bibliography on copy number variations (programs)
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front page
2008
2007
2006
2005
2004
2003
2002
2001
2000
90s
glossary
links
programs
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ADaCGH : similar to SW-ARRAY and CRAN/cgh
http://adacgh2.bioinfo.cnio.es/
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Affymetrix Genotyping Console Software : from Affymetrix [USA]
http://www.affymetrix.com/products/software/
specific/genotyping_console_software.affx
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Agilent CGH Analytics 3.5 software : from Agilent [USA]
http://www.chem.agilent.com/Scripts/PDS.asp?lPage=29457
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Bioconductor: one can find several R packages here,
aCGH, CGHcall , cghMCR, DNAcopy ,
GLAD, ITALICS, MANOR , SMAP , snapCGH
http://www.bioconductor.org/packages/release/Software.html
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CAPweb : from Institut Curie Bioinformatics Unit
[France]
http://bioinfo-out.curie.fr/CAPweb/
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CGHcall: from VU Medisch Centrum [Netherlands]
http://www.few.vu.nl/~mavdwiel/CGHcall.html
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CGHmix: from Department of Epidemiology and Public Health,
Imperial College Norfolk Place [UK]
http://www.bgx.org.uk/software.html
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CGHScan: from Animal Health and Biomedical Sciences,
University of Wisconsin [USA]
http://gel.ahabs.wisc.edu/cghscan/
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CGHweb: from the Children's Hospital Informatics Program,
and Harvard-Partners Center for Genomics and Genetics
[USA]
http://compbio.med.harvard.edu/CGHweb/
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CNIT : [Taiwan]
http://140.109.41.16/EAG/Program%20list/CNIT.htm
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CNVphaser: from RIKEN [Japan]
http://emu.src.riken.jp/
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CNVtools : from Sanger Institute [UK]
http://cnv-tools.sourceforge.net/
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CRAN : contributed R packages, may contain some
relevant packages not listed in Bioconductor, such as
RJaCGH,
cgh ,
cghFLasso ,
clac
http://cran.r-project.org/web/packages/
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dChip: from Department of Biostatistics, Harvard University
[USA]
http://biosun1.harvard.edu/complab/dchip/copy.htm
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GEAR : from Department of Microbiology,
The Catholic University of Korea [Korea]
http://www.systemsbiology.co.kr/GEAR/
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GLAD : from Institut Curie Bioinformatics Unit
[France]
documentation can be found here
http://bioinfo-out.curie.fr/projects/glad/
and request sent to glad@curie.fr
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Golden Helix, Copy Number Analysis Module: from Golden Helix [USA]
http://goldenhelix.com/SNP_Variation/CNAM/index.html
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Illumina BeadStudio Genotyping Module : from Illumina [USA]
http://www.illumina.com/pages.ilmn?ID=169
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ImaGene CGH : from BioDiscovery [USA]
http://www.biodiscovery.com/index/imagene-cgh
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ISACGH : from Bioinformatics Department,
Centro de Investigación Príncipe Felipe [Spain]
http://isacgh.bioinfo.cipf.es/
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MANOR: from Institut Curie Bioinformatics Unit
[France]
documentation can be found here
http://bioinfo-out.curie.fr/projects/manor/
and request sent to manor@curie.fr
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NimbleScan : from Roche NimbleGen (in version 2.4,
either the DNACopy v1.4 algorithm or the segMNT v1.1 algorithm
is used) [USA]
http://www.nimblegen.com/products/software/index.html
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Partek Genomic Suite: from Partek [USA]
http://www.partek.com/partekgs_copynumber
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PennCNV : from Department of Genetics, University of Pennsylvania [USA]
http://www.neurogenome.org/cnv/penncnv/
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QuantiSNP : from Department of Statistics, University of Oxford
and the Wellcome Trust Centre for Human Genetics. [UK]
http://www.well.ox.ac.uk/QuantiSNP/
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smoothseg : from Department of Medical Epidemiology and Biostatistics ,
Karolinska Institutet
http://www.meb.ki.se/~yudpaw/
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STAC : from Genomics Institute, University of Pennsylvania [USA]
http://cbil.upenn.edu/STAC/
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SW-ARRAY:
http://sgdp.iop.kcl.ac.uk/tprice/software.html
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VAMP: from Institut Curie Bioinformatics Unit
[France]
http://bioinfo-out.curie.fr/actudb/
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