GeneTrack - a genomic data processing and visualization framework
被引:76
作者:
Albert, Istvan
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Penn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA
Penn State Univ, Ctr Comparat Genom & Bioinformat, Ctr Gene Regulat, University Pk, PA 16802 USA
Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA
Albert, Istvan
[1
,2
,3
]
Wachi, Shinichiro
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机构:
Penn State Univ, Ctr Comparat Genom & Bioinformat, Ctr Gene Regulat, University Pk, PA 16802 USA
Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA
Wachi, Shinichiro
[2
,3
]
Jiang, Cizhong
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机构:
Penn State Univ, Ctr Comparat Genom & Bioinformat, Ctr Gene Regulat, University Pk, PA 16802 USA
Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA
Jiang, Cizhong
[2
,3
]
Pugh, Franklin
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机构:
Penn State Univ, Ctr Comparat Genom & Bioinformat, Ctr Gene Regulat, University Pk, PA 16802 USA
Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA
Pugh, Franklin
[2
,3
]
机构:
[1] Penn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA
[2] Penn State Univ, Ctr Comparat Genom & Bioinformat, Ctr Gene Regulat, University Pk, PA 16802 USA
[3] Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USA
Motivation: High-throughput ChIP-chip and ChIP-seq methodologies generate sufficiently large data sets that analysis poses significant informatics challenges, particularly for research groups with modest computational support. To address this challenge, we devised a software platform for storing, analyzing and visualizing high resolution genome-wide binding data. GeneTrack automates several steps of a typical data processing pipeline, including smoothing and peak detection, and facilitates dissemination of the results via the web. Our software is freely available via the Google Project Hosting environment at http://genetrack.googlecode.com.
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Albert, Istvan
;
Mavrich, Travis N.
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Mavrich, Travis N.
;
Tomsho, Lynn P.
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Tomsho, Lynn P.
;
Qi, Ji
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Qi, Ji
;
Zanton, Sara J.
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Zanton, Sara J.
;
Schuster, Stephan C.
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Schuster, Stephan C.
;
Pugh, B. Franklin
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机构:
Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Blankenberg, Daniel
;
Taylor, James
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Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Taylor, James
;
Schenck, Ian
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Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Schenck, Ian
;
He, Jianbin
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Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
He, Jianbin
;
Zhang, Yi
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Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Zhang, Yi
;
Ghent, Matthew
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Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Ghent, Matthew
;
Veeraraghavan, Narayanan
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Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Veeraraghavan, Narayanan
;
Albert, Istvan
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Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Albert, Istvan
;
Miller, Webb
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Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Miller, Webb
;
Makova, Kateryna D.
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Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Makova, Kateryna D.
;
Hardison, Ross C.
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Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Hardison, Ross C.
;
Nekrutenko, Anton
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Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
机构:
Univ Calif Santa Cruz, Dept Mol Cellular & Dev Biol, Santa Cruz, CA 95064 USAUniv Calif Santa Cruz, Dept Mol Cellular & Dev Biol, Santa Cruz, CA 95064 USA
Kent, WJ
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Sugnet, CW
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机构:Univ Calif Santa Cruz, Dept Mol Cellular & Dev Biol, Santa Cruz, CA 95064 USA
Sugnet, CW
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Furey, TS
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机构:Univ Calif Santa Cruz, Dept Mol Cellular & Dev Biol, Santa Cruz, CA 95064 USA
Furey, TS
;
Roskin, KM
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机构:Univ Calif Santa Cruz, Dept Mol Cellular & Dev Biol, Santa Cruz, CA 95064 USA
Roskin, KM
;
Pringle, TH
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机构:Univ Calif Santa Cruz, Dept Mol Cellular & Dev Biol, Santa Cruz, CA 95064 USA
Pringle, TH
;
Zahler, AM
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机构:Univ Calif Santa Cruz, Dept Mol Cellular & Dev Biol, Santa Cruz, CA 95064 USA
Zahler, AM
;
Haussler, D
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机构:Univ Calif Santa Cruz, Dept Mol Cellular & Dev Biol, Santa Cruz, CA 95064 USA
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Albert, Istvan
;
Mavrich, Travis N.
论文数: 0引用数: 0
h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Mavrich, Travis N.
;
Tomsho, Lynn P.
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Tomsho, Lynn P.
;
Qi, Ji
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Qi, Ji
;
Zanton, Sara J.
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Zanton, Sara J.
;
Schuster, Stephan C.
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h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Schuster, Stephan C.
;
Pugh, B. Franklin
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h-index: 0
机构:
Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Blankenberg, Daniel
;
Taylor, James
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h-index: 0
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Taylor, James
;
Schenck, Ian
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机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Schenck, Ian
;
He, Jianbin
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机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
He, Jianbin
;
Zhang, Yi
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机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Zhang, Yi
;
Ghent, Matthew
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机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Ghent, Matthew
;
Veeraraghavan, Narayanan
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Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Veeraraghavan, Narayanan
;
Albert, Istvan
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Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Albert, Istvan
;
Miller, Webb
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机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Miller, Webb
;
Makova, Kateryna D.
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h-index: 0
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Makova, Kateryna D.
;
Hardison, Ross C.
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Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Hardison, Ross C.
;
Nekrutenko, Anton
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机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
机构:
Univ Calif Santa Cruz, Dept Mol Cellular & Dev Biol, Santa Cruz, CA 95064 USAUniv Calif Santa Cruz, Dept Mol Cellular & Dev Biol, Santa Cruz, CA 95064 USA
Kent, WJ
;
Sugnet, CW
论文数: 0引用数: 0
h-index: 0
机构:Univ Calif Santa Cruz, Dept Mol Cellular & Dev Biol, Santa Cruz, CA 95064 USA
Sugnet, CW
;
Furey, TS
论文数: 0引用数: 0
h-index: 0
机构:Univ Calif Santa Cruz, Dept Mol Cellular & Dev Biol, Santa Cruz, CA 95064 USA
Furey, TS
;
Roskin, KM
论文数: 0引用数: 0
h-index: 0
机构:Univ Calif Santa Cruz, Dept Mol Cellular & Dev Biol, Santa Cruz, CA 95064 USA
Roskin, KM
;
Pringle, TH
论文数: 0引用数: 0
h-index: 0
机构:Univ Calif Santa Cruz, Dept Mol Cellular & Dev Biol, Santa Cruz, CA 95064 USA
Pringle, TH
;
Zahler, AM
论文数: 0引用数: 0
h-index: 0
机构:Univ Calif Santa Cruz, Dept Mol Cellular & Dev Biol, Santa Cruz, CA 95064 USA
Zahler, AM
;
Haussler, D
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h-index: 0
机构:Univ Calif Santa Cruz, Dept Mol Cellular & Dev Biol, Santa Cruz, CA 95064 USA