Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x
Associations between DNA polymorphisms and mRNA abundance are a natural target of genetic investigations, and microarrays facilitate genome-wide and transcriptome-wide surveys of these associations. This work is motivated by emerging requirements for data architectures and algorithm interfaces to al...
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| Published in | Bioinformatics Vol. 25; no. 11; pp. 1447 - 1448 |
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| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Oxford
Oxford University Press
01.06.2009
Oxford Publishing Limited (England) |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1367-4803 1367-4811 1460-2059 1367-4811 |
| DOI | 10.1093/bioinformatics/btp169 |
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| Abstract | Associations between DNA polymorphisms and mRNA abundance are a natural target of genetic investigations, and microarrays facilitate genome-wide and transcriptome-wide surveys of these associations. This work is motivated by emerging requirements for data architectures and algorithm interfaces to allow flexible exploration of public and private archives of genotyping and expression arrays. Using R/Bioconductor facilities, Phase II HapMap genotypes and Illumina 47K expression assay results archived on multiple populations may be interactively explored and analyzed using commodity hardware. Availability and Implementation: Open Source. Bioconductor 2.3 packages GGtools, GGBase, GGdata, hmyriB36. Freely available on the web at http://www.bioconductor.org Contact: stvjc@channing.harvard.edu |
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| AbstractList | Associations between DNA polymorphisms and mRNA abundance are a natural target of genetic investigations, and microarrays facilitate genome-wide and transcriptome-wide surveys of these associations. This work is motivated by emerging requirements for data architectures and algorithm interfaces to allow flexible exploration of public and private archives of genotyping and expression arrays. Using R/Bioconductor facilities, Phase II HapMap genotypes and Illumina 47K expression assay results archived on multiple populations may be interactively explored and analyzed using commodity hardware.
Availability and Implementation: Open Source. Bioconductor 2.3 packages GGtools, GGBase, GGdata, hmyriB36. Freely available on the web at http://www.bioconductor.org
Contact: stvjc@channing.harvard.edu Associations between DNA polymorphisms and mRNA abundance are a natural target of genetic investigations, and microarrays facilitate genome-wide and transcriptome-wide surveys of these associations. This work is motivated by emerging requirements for data architectures and algorithm interfaces to allow flexible exploration of public and private archives of genotyping and expression arrays. Using R/Bioconductor facilities, Phase II HapMap genotypes and Illumina 47K expression assay results archived on multiple populations may be interactively explored and analyzed using commodity hardware. Availability and Implementation: Open Source. Bioconductor 2.3 packages GGtools, GGBase, GGdata, hmyriB36. Freely available on the web at http://www.bioconductor.org Contact: stvjc@channing.harvard.edu Associations between DNA polymorphisms and mRNA abundance are a natural target of genetic investigations, and microarrays facilitate genome-wide and transcriptome-wide surveys of these associations. This work is motivated by emerging requirements for data architectures and algorithm interfaces to allow flexible exploration of public and private archives of genotyping and expression arrays. Using R-Bioconductor facilities, Phase II HapMap genotypes and Illumina 47K expression assay results archived on multiple populations may be interactively explored and analyzed using commodity hardware.Availability and Implementation: Open Source. Bioconductor 2.3 packages GGtools, GGBase, GGdata, hmyriB36. Freely available on the web at http://www.bioconductor.orgContact: stvjcatchanning.harvard.edu Associations between DNA polymorphisms and mRNA abundance are a natural target of genetic investigations, and microarrays facilitate genome-wide and transcriptome-wide surveys of these associations. This work is motivated by emerging requirements for data architectures and algorithm interfaces to allow flexible exploration of public and private archives of genotyping and expression arrays. Using R/Bioconductor facilities, Phase II HapMap genotypes and Illumina 47K expression assay results archived on multiple populations may be interactively explored and analyzed using commodity hardware. Open Source. Bioconductor 2.3 packages GGtools, GGBase, GGdata, hmyriB36. Freely available on the web at (http://www.bioconductor.org). Associations between DNA polymorphisms and mRNA abundance are a natural target of genetic investigations, and microarrays facilitate genome-wide and transcriptome-wide surveys of these associations. This work is motivated by emerging requirements for data architectures and algorithm interfaces to allow flexible exploration of public and private archives of genotyping and expression arrays. Using R Bioconductor facilities, Phase II HapMap genotypes and Illumina 47K expression assay results archived on multiple populations may be interactively explored and analyzed using commodity hardware. Availability and Implementation: Open Source. Bioconductor 2.3 packages GGtools, GGBase, GGdata, hmyriB36. Freely available on the web at http://www.bioconductor.org Contact: stvjc@channing.harvard.edu Associations between DNA polymorphisms and mRNA abundance are a natural target of genetic investigations, and microarrays facilitate genome-wide and transcriptome-wide surveys of these associations. This work is motivated by emerging requirements for data architectures and algorithm interfaces to allow flexible exploration of public and private archives of genotyping and expression arrays. Using R/Bioconductor facilities, Phase II HapMap genotypes and Illumina 47K expression assay results archived on multiple populations may be interactively explored and analyzed using commodity hardware.SUMMARYAssociations between DNA polymorphisms and mRNA abundance are a natural target of genetic investigations, and microarrays facilitate genome-wide and transcriptome-wide surveys of these associations. This work is motivated by emerging requirements for data architectures and algorithm interfaces to allow flexible exploration of public and private archives of genotyping and expression arrays. Using R/Bioconductor facilities, Phase II HapMap genotypes and Illumina 47K expression assay results archived on multiple populations may be interactively explored and analyzed using commodity hardware.Open Source. Bioconductor 2.3 packages GGtools, GGBase, GGdata, hmyriB36. Freely available on the web at (http://www.bioconductor.org).AVAILABILITY AND IMPLEMENTATIONOpen Source. Bioconductor 2.3 packages GGtools, GGBase, GGdata, hmyriB36. Freely available on the web at (http://www.bioconductor.org). |
| Author | Gentleman, Robert Davis, Adam R. Carey, Vincent J. Lawrence, Michael F. Raby, Benjamin A. |
| AuthorAffiliation | 1 Channing Laboratory, Department of Medicine, 2 I2B2 National Center for Biocomputing, Brigham and Women's Hospital, 75 Francis St. Boston MA 02115 and 3 Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA |
| AuthorAffiliation_xml | – name: 1 Channing Laboratory, Department of Medicine, 2 I2B2 National Center for Biocomputing, Brigham and Women's Hospital, 75 Francis St. Boston MA 02115 and 3 Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA |
| Author_xml | – sequence: 1 givenname: Vincent J. surname: Carey fullname: Carey, Vincent J. organization: Channing Laboratory, Department of Medicine, I2B2 National Center for Biocomputing, Brigham and Women's Hospital, 75 Francis St. Boston MA 02115 and Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA – sequence: 2 givenname: Adam R. surname: Davis fullname: Davis, Adam R. organization: Channing Laboratory, Department of Medicine, I2B2 National Center for Biocomputing, Brigham and Women's Hospital, 75 Francis St. Boston MA 02115 and Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA – sequence: 3 givenname: Michael F. surname: Lawrence fullname: Lawrence, Michael F. organization: Channing Laboratory, Department of Medicine, I2B2 National Center for Biocomputing, Brigham and Women's Hospital, 75 Francis St. Boston MA 02115 and Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA – sequence: 4 givenname: Robert surname: Gentleman fullname: Gentleman, Robert organization: Channing Laboratory, Department of Medicine, I2B2 National Center for Biocomputing, Brigham and Women's Hospital, 75 Francis St. Boston MA 02115 and Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA – sequence: 5 givenname: Benjamin A. surname: Raby fullname: Raby, Benjamin A. organization: Channing Laboratory, Department of Medicine, I2B2 National Center for Biocomputing, Brigham and Women's Hospital, 75 Francis St. Boston MA 02115 and Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA |
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| Cites_doi | 10.1038/ng2119 10.1101/gr.6981507 10.1159/000101422 10.1038/ng2109 10.1038/ng2142 10.1371/journal.pbio.0060107 |
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| Copyright | The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org 2009 2009 INIST-CNRS The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org |
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| Keywords | Data analysis Gene Genetic algorithm Genetics Data Gene expression Data structure |
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| References | Williams (2023013111495217200_B7) 2007; 17 Stranger (2023013111495217200_B6) 2007; 39 Clayton (2023013111495217200_B2) 2007; 64 Schadt (2023013111495217200_B5) 2008; 6 Cheung (2023013111495217200_B1) 2005; 437 Göring (2023013111495217200_B4) 2007; 39 Dixon (2023013111495217200_B3) 2007; 39 17483596 - Hum Hered. 2007;64(1):45-51 17873874 - Nat Genet. 2007 Oct;39(10):1217-24 18462017 - PLoS Biol. 2008 May 6;6(5):e107 16251966 - Nature. 2005 Oct 27;437(7063):1365-9 17873877 - Nat Genet. 2007 Oct;39(10):1202-7 17873875 - Nat Genet. 2007 Oct;39(10):1208-16 18063559 - Genome Res. 2007 Dec;17(12):1707-16 |
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| SubjectTerms | Algorithms Applications Note Biological and medical sciences Databases, Genetic Fundamental and applied biological sciences. Psychology Gene Expression Profiling - methods General aspects Genetics Genotype Genotypes Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Oligonucleotide Array Sequence Analysis - methods Polymorphism, Single Nucleotide Software |
| Title | Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x |
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