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1 <html>
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2 <head>
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3 </head>
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4 <body>
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5 <h1><a target='_top' href='http://cran.r-project.org/web/packages/sequenza/index.html'>Sequenza</a> - results</h1>
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6 <p align='center'>
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7 <table width=70% border=1>
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8 <font size='30pt'><tr>
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9 <th colspan=3>Additional files</th>
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10 </tr>
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11 <tr>
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12 <td><a href='out.seqz.gz'>Out Sequenza</a><br><a href='out.small.seqz.gz'>Out small Sequenza</a></td>
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13 <td><a href='sample_sequenza_cp_table.RData'>Cellularity and ploidy matrix (RData)</a><br><a href='sample_sequenza_extract.RData'>Sequenza extract (RData)</a></td><td><a href='logFile.txt'>Log file</a><br><a href='all_files.tar.gz'>All files</a></td>
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14 </tr>
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15 </font>
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16 </table>
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17 </p>
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18 <h2>Genome-wide view of the allele and copy number state</h2>
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19 <p align='center'><embed src='sample_analyse.pdf' width='800px' height='590px'></p>
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20 <p align='center'>Genome-wide allele-specific copy number profile obtained from exome sequencing (top), genome-wide absolute copy number profile obtained from exome sequencing (middle) and depth ratio (bottom).</p>
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21 <p align='center'>File (best solution or user solution): <a href='sample_segments.txt'>Segments</a></p>
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22 <p align='center'>File (alternative solutions): <a href='sample_segments.tar.gz'>Segments</a></p>
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23 <p align='center'>File : <a href='sample_mutations.txt'>Mutations</a></p>
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24 <h2>Confidence intervals, confidence region and point estimate</h2>
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25 <p align='center'><embed src='sample_CP_contours.pdf' width='580px' height='580px'></p>
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26 <p align='center'>Result from the inference over the defined range of cellularity and ploidy. Color intensity indicates the log posterior probability of corresponding cellularity/ploidy values.</p>
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27 <p align='center'><embed src='sample_CN_bars.pdf' width='580px' height='580px'></p>
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28 <p align='center'><embed src='sample_model_fit.pdf' width='580px' height='580px'></p>
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29 <p align='center'>Observed depth ratio and BAF values for each genomic segment (black circles and dots) along with the representative joint LPP density (colors). The representative joint LPP density is calculated for the best cellularity and ploidy.</p>
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30 <p align='center'>File : <a href='sample_cellularity_ploidy.txt'>Cellularity and ploidy</a></p>
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31 <p align='center'><embed src='sample_alternative_fit.pdf' width='580px' height='580px'></p>
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32 <p align='center'>Observed depth ratio and BAF values for each genomic segment (black circles and dots) along with the representative joint LPP density (colors). The representative joint LPP density is calculated for the alternative cellularity and ploidy (scroll).</p>
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33 <p align='center'>File : <a href='sample_alternative_solutions.txt'>Alternative solutions</a></p>
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34 <h2>Normalization of depth ratio</h2>
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35 <p align='center'><a href='sample_gc_stat.png'><img border='1' width='680px height='300px src='sample_gc_stat.png'></a></p>
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36 <p align='center'>Visualization of depth.ratio bias in relation of GC content (left), and resulting normalization effect (right)</p>
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37 <h2>Plot chromosome view with mutations, BAF, depth ratio and segments (best solution or user solution)</h2>
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38 <p align='center'><embed src='sample_chromosome_view.pdf' width='680px' height='680px'></p>
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39 <p align='center'>Plots of mutant allele frequency (top), B allele frequency (middle) and depth ratio (bottom) vs. chromosome position (scroll).</p>
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40 </body>
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41 </html> |
