Dalliance Genome Explorer

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(ページの作成: * サイト:http://www.biodalliance.org/ * デモ:http://www.biodalliance.org/human/ncbi36/ -- NCBI36 * 技術:JavaScript, SVG, DAS * 論文:http://bioinformatics.oxfordj...)
 
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* 論文:http://bioinformatics.oxfordjournals.org/content/early/2011/01/19/bioinformatics.btr020.abstract
* 論文:http://bioinformatics.oxfordjournals.org/content/early/2011/01/19/bioinformatics.btr020.abstract
* ソースコード:https://github.com/dasmoth/dalliance
* ソースコード:https://github.com/dasmoth/dalliance
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== コード例 ==
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* http://www.biodalliance.org/human/ncbi36/ -- NCBI36
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<pre>
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<script language="javascript" src="/js/dalliance-compiled.js"></script>
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<script language="javascript">
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  new Browser({
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      chr:          '22',
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      viewStart:    30000000,
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      viewEnd:      30030000,
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      cookieKey:    'human',
 +
 +
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    chains: {
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      hg19ToHg18: new Chainset('http://www.derkholm.net:8080/das/hg19ToHg18/', 'GRCh37', 'NCBI36',
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                              {
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                                  speciesName: 'Human',
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                                  taxon: 9606,
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                                  auth: 'GRCh',
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                                  version: 37
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                              })
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    },
 +
 +
      sources:    [{name: 'Genome',
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                    uri:  'http://www.derkholm.net:8080/das/hg18comp/',
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                    desc: 'Human reference genome build NCBI36',
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                    tier_type: 'sequence',
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                    provides_entrypoints: true},
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                    {name: 'Genes',
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                    desc: 'Gene structures from Ensembl 54',
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                    uri:  'http://www.derkholm.net:8080/das/hsa_54_36p/',
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                    collapseSuperGroups: true,
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                    provides_karyotype: true,
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                    provides_search: true},
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                    {name: 'Repeats',
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                    desc: 'Repeat annotation from Ensembl 54',
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                    uri: 'http://www.derkholm.net:8080/das/hsa_54_36p/',
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                    stylesheet_uri: 'http://www.derkholm.net/dalliance-test/stylesheets/ens-repeats.xml'},
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                    {name: 'CpG',
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                    desc: 'CpG observed/expected ratio',
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                    uri: 'http://www.derkholm.net:8080/das/hg18comp/',
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                    stylesheet_uri: 'http://www.derkholm.net/dalliance-test/stylesheets/cpg.xml'},
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                    {name: 'MeDIP-raw',
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                    desc: 'MeDIP-seq reads from Nature Biotech. 26:779-785',
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                    uri: 'http://www.derkholm.net:8080/das/medipseq_reads/'},
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                    {name: 'MeDIP-seq',
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                    desc: 'Human sperm MeDIP-seq (Batman normalized) from Nature Biotech. 26:779-785',
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                    uri:  'http://www.ebi.ac.uk/das-srv/genomicdas/das/batman_seq_SP/'},
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                    {name: 'MeDIP-chip',
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                    desc: 'Huamn sperm MeDIP-chip (Batman-normalized)',
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                    uri: 'http://www.ebi.ac.uk/das-srv/genomicdas/das/batman_SP/'}],
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      browserLinks: {
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            Ensembl: 'http://ncbi36.ensembl.org/Homo_sapiens/Location/View?r=${chr}:${start}-${end}',
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            UCSC: 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr${chr}:${start}-${end}'
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      },
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    searchEndpoint: new DASSource('http://www.derkholm.net:8080/das/hsa_54_36p/')
 +
  });
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</script>
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 +
<div id='svgHolder'></div>
 +
</pre>
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 +
[[Category:データ可視化]]

2011年1月24日 (月) 02:22時点における最新版

コード例

<script language="javascript" src="/js/dalliance-compiled.js"></script> 
<script language="javascript"> 
  new Browser({
      chr:          '22',
      viewStart:    30000000,
      viewEnd:      30030000,
      cookieKey:    'human',
 
 
    chains: {
      hg19ToHg18: new Chainset('http://www.derkholm.net:8080/das/hg19ToHg18/', 'GRCh37', 'NCBI36',
                               {
                                  speciesName: 'Human',
                                  taxon: 9606,
                                  auth: 'GRCh',
                                  version: 37
                               })
    },
 
      sources:     [{name: 'Genome',
                     uri:  'http://www.derkholm.net:8080/das/hg18comp/',
                     desc: 'Human reference genome build NCBI36',
                     tier_type: 'sequence',
                     provides_entrypoints: true},
                    {name: 'Genes',
                     desc: 'Gene structures from Ensembl 54',
                     uri:  'http://www.derkholm.net:8080/das/hsa_54_36p/',
                     collapseSuperGroups: true,
                     provides_karyotype: true,
                     provides_search: true},
                    {name: 'Repeats',
                     desc: 'Repeat annotation from Ensembl 54',
                     uri: 'http://www.derkholm.net:8080/das/hsa_54_36p/',
                     stylesheet_uri: 'http://www.derkholm.net/dalliance-test/stylesheets/ens-repeats.xml'},
                    {name: 'CpG',
                     desc: 'CpG observed/expected ratio',
                     uri: 'http://www.derkholm.net:8080/das/hg18comp/',
                     stylesheet_uri: 'http://www.derkholm.net/dalliance-test/stylesheets/cpg.xml'},
                    {name: 'MeDIP-raw',
                     desc: 'MeDIP-seq reads from Nature Biotech. 26:779-785',
                     uri: 'http://www.derkholm.net:8080/das/medipseq_reads/'},
                    {name: 'MeDIP-seq',
                     desc: 'Human sperm MeDIP-seq (Batman normalized) from Nature Biotech. 26:779-785',
                     uri:  'http://www.ebi.ac.uk/das-srv/genomicdas/das/batman_seq_SP/'},
                    {name: 'MeDIP-chip',
                     desc: 'Huamn sperm MeDIP-chip (Batman-normalized)',
                     uri: 'http://www.ebi.ac.uk/das-srv/genomicdas/das/batman_SP/'}],
 
       browserLinks: {
            Ensembl: 'http://ncbi36.ensembl.org/Homo_sapiens/Location/View?r=${chr}:${start}-${end}',
            UCSC: 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr${chr}:${start}-${end}'
       },
 
     searchEndpoint: new DASSource('http://www.derkholm.net:8080/das/hsa_54_36p/')
  });
</script> 

<div id='svgHolder'></div>
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