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3 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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4 <meta name="generator" content="Galaxy rgToolFactory.py tool output - see http://getgalaxy.org/" />
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5 <title></title>
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6 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
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7 </head>
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8 <body>
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9 <div class="toolFormBody">
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11 <div class="infomessage">Galaxy Tool "Differential_Counts" run at 28/12/2014 21:02:37</div><br/>
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12 <div class="toolFormTitle">DESeq2 images and outputs</div>
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13 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
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14 <div><table class="simple" cellpadding="2" cellspacing="2">
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15 <tr>
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16 <td><a href="DESeq2_edgeRtest_MA_plot.pdf"><img src="DESeq2_edgeRtest_MA_plot.png" title="Click to download a PDF of DESeq2_edgeRtest_MA_plot.pdf" hspace="5" width="400"
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17 alt="Image called DESeq2_edgeRtest_MA_plot.pdf"/></a></td>
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19 <td><a href="DESeq2_edgeRtest_PCA_plot.pdf"><img src="DESeq2_edgeRtest_PCA_plot.png" title="Click to download a PDF of DESeq2_edgeRtest_PCA_plot.pdf" hspace="5" width="400"
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20 alt="Image called DESeq2_edgeRtest_PCA_plot.pdf"/></a></td>
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22 <td><a href="DESeq2_edgeRtest_dispersion_estimates.pdf"><img src="DESeq2_edgeRtest_dispersion_estimates.png" title="Click to download a PDF of DESeq2_edgeRtest_dispersion_estimates.pdf" hspace="5" width="400"
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23 alt="Image called DESeq2_edgeRtest_dispersion_estimates.pdf"/></a></td>
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24 </tr>
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25 <tr>
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26 <td><a href="DESeq2_edgeRtest_qqplot.pdf"><img src="DESeq2_edgeRtest_qqplot.png" title="Click to download a PDF of DESeq2_edgeRtest_qqplot.pdf" hspace="5" width="400"
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27 alt="Image called DESeq2_edgeRtest_qqplot.pdf"/></a></td>
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29 <td><a href="DESeq2_edgeRtest_sample_distance_plot.pdf"><img src="DESeq2_edgeRtest_sample_distance_plot.png" title="Click to download a PDF of DESeq2_edgeRtest_sample_distance_plot.pdf" hspace="5" width="400"
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30 alt="Image called DESeq2_edgeRtest_sample_distance_plot.pdf"/></a></td>
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31
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32 <td> </td>
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33 </tr></table></div>
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34
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35 <div class="toolFormTitle">DESeq2 log output</div>
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36
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37 <pre>
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38
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39 # DESeq top 50
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40
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41 Contig baseMean log2FoldChange lfcSE stat pvalue padj NReads URL
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42
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43 Mir192 Mir192 271352.97636 6.965264 0.2150593 32.387646 4.096935e-230 3.818343e-227 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
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44
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45 Mir122a Mir122a 10112.31117 10.312083 0.3292695 31.318061 2.649329e-215 1.234587e-212 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
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46
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47 Mir149 Mir149 810.35429 -6.911118 0.2341392 -29.517132 1.735536e-191 5.391733e-189 6164 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a>
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48
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49 Mir23a Mir23a 1289.18043 -3.104086 0.1191688 -26.047815 1.424245e-149 3.318491e-147 10118 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a>
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50
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51 Mir181d Mir181d 275.22797 -3.581172 0.1778187 -20.139461 3.329373e-90 6.205952e-88 2139 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a>
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52
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53 Mir204 Mir204 347.57397 -7.284200 0.3771119 -19.315751 3.959346e-83 6.150183e-81 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
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54
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55 Mir23b Mir23b 2028.55377 -2.065110 0.1085802 -19.019217 1.182361e-80 1.574229e-78 16387 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a>
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56
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57 Mir27a Mir27a 2788.72629 -3.016676 0.1688167 -17.869539 2.036708e-71 2.372765e-69 21886 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
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58
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59 Mir195 Mir195 519.86200 -3.152795 0.1784796 -17.664734 7.838131e-70 8.116820e-68 3962 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a>
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60
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61 Mir194-2 Mir194-2 391.65678 5.222911 0.3099275 16.852045 1.013492e-63 9.445744e-62 3570 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a>
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62
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63 Mir208b Mir208b 1649.77924 -11.396172 0.6771238 -16.830264 1.464482e-63 1.240816e-61 14756 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
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64
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65 Mir10b Mir10b 27820.40551 -5.071453 0.3044884 -16.655656 2.753110e-62 2.138249e-60 197340 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
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66
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67 Mir181c Mir181c 2765.96510 -3.660964 0.2275711 -16.087120 3.141152e-58 2.251965e-56 23605 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
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68
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69 Mir208a Mir208a 616.76981 -10.356524 0.6559218 -15.789267 3.688391e-56 2.455415e-54 4638 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a>
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70
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71 Mir490 Mir490 220.99790 -8.059660 0.5142876 -15.671504 2.369067e-55 1.471980e-53 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
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72
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73 Mir203 Mir203 772.92882 1.990849 0.1274099 15.625546 4.877239e-55 2.840992e-53 6739 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a>
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74
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75 Mir215 Mir215 152.78082 -3.004380 0.1939090 -15.493765 3.822341e-54 2.095542e-52 1182 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'>Mir215</a>
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76
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77 Dnm3os Dnm3os 179.61643 -3.278392 0.2166491 -15.132265 9.922045e-52 5.137415e-50 1401 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'>Dnm3os</a>
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78
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79 Mir214 Mir214 134.69038 -3.216444 0.2154916 -14.926074 2.230149e-50 1.093947e-48 1048 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a>
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80
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81 Mir21 Mir21 26121.31011 2.963903 0.2008617 14.755939 2.817433e-49 1.312924e-47 229120 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
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82
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83 Mir1948 Mir1948 263.89527 7.074045 0.4867226 14.534039 7.374076e-48 3.272685e-46 2404 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a>
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84
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85 Mir27b Mir27b 76478.05753 -1.904653 0.1312889 -14.507339 1.088626e-47 4.611815e-46 625308 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27b'>Mir27b</a>
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86
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87 Rabggtb Rabggtb 2257.19195 1.988368 0.1401741 14.184987 1.134862e-45 4.598659e-44 19535 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
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88
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89 Mir499 Mir499 712.45950 -10.577061 0.7528467 -14.049423 7.766426e-45 3.015962e-43 6527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
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90
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91 Mir101b Mir101b 6846.19683 3.791681 0.2809666 13.495132 1.670548e-41 6.227801e-40 59019 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
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92
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93 Mir132 Mir132 106.46062 -2.797928 0.2083376 -13.429779 4.046171e-41 1.450397e-39 857 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'>Mir132</a>
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94
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95 Mir143hg Mir143hg 180217.77425 -2.169143 0.1685614 -12.868566 6.764677e-38 2.335066e-36 1407364 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143hg'>Mir143hg</a>
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96
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97 Mir143 Mir143 179219.35960 -2.170303 0.1696199 -12.795094 1.746402e-37 5.813025e-36 1399819 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143'>Mir143</a>
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98
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99 Mir155 Mir155 57.66182 -3.788079 0.3056585 -12.393175 2.845516e-35 9.144898e-34 463 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a>
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100
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101 Mir322 Mir322 899.53469 -3.126011 0.2622596 -11.919531 9.363380e-33 2.908890e-31 7074 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a>
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102
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103 Mir378 Mir378 483.21548 -2.994300 0.2577321 -11.617876 3.343461e-31 1.005195e-29 4075 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a>
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104
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105 Mir24-2 Mir24-2 424.48288 -2.712674 0.2361028 -11.489378 1.491830e-30 4.213289e-29 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'>Mir24-2</a>
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106
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107 Mir3074-2 Mir3074-2 424.48288 -2.712674 0.2361028 -11.489378 1.491830e-30 4.213289e-29 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'>Mir3074-2</a>
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108
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109 Mir199b Mir199b 47.84725 -5.294373 0.4644474 -11.399295 4.215163e-30 1.155451e-28 370 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a>
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110
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111 Mir802 Mir802 166.83414 8.816580 0.7782636 11.328527 9.478530e-30 2.523997e-28 1514 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
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112
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113 Mir125b-2 Mir125b-2 493.08516 -2.919341 0.2631193 -11.095122 1.324798e-28 3.429754e-27 3837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a>
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114
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115 Mir301 Mir301 260.53406 -1.676984 0.1526772 -10.983852 4.570133e-28 1.151179e-26 2119 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir301'>Mir301</a>
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116
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117 Snord104 Snord104 3851.90119 2.386573 0.2173857 10.978522 4.847915e-28 1.189015e-26 33458 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
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118
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119 Mir150 Mir150 553.20599 -2.836881 0.2595088 -10.931734 8.127991e-28 1.942381e-26 4229 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir150'>Mir150</a>
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120
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121 Mir148a Mir148a 118994.46955 2.678852 0.2481801 10.793984 3.675045e-27 8.562855e-26 1002397 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'>Mir148a</a>
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122
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123 5430416N02Rik 5430416N02Rik 62.15966 3.089960 0.2941123 10.506053 8.101331e-26 1.841571e-24 564 <a href='http://www.genecards.org/index.php?path=/Search/keyword/5430416N02Rik'>5430416N02Rik</a>
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124
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125 Mir193 Mir193 45.70861 4.991530 0.4814098 10.368568 3.446495e-25 7.647936e-24 421 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193'>Mir193</a>
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126
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127 Mir3073 Mir3073 98.93199 8.208709 0.7944742 10.332254 5.036321e-25 1.091593e-23 904 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a>
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128
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129 Mir125b-1 Mir125b-1 79.01988 -3.020660 0.2937360 -10.283590 8.355635e-25 1.769875e-23 609 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-1'>Mir125b-1</a>
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130
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131 2610203C20Rik 2610203C20Rik 79.17666 -3.023491 0.2948614 -10.253939 1.136165e-24 2.353124e-23 610 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2610203C20Rik'>2610203C20Rik</a>
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132
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133 Mir181a-1 Mir181a-1 59.53826 -3.151487 0.3211628 -9.812740 9.923710e-23 2.010630e-21 506 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-1'>Mir181a-1</a>
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134
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135 Mir184 Mir184 32.23796 -4.865023 0.4962776 -9.803028 1.092606e-22 2.166615e-21 247 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a>
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136
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137 Mir199a-2 Mir199a-2 44.84878 -3.422216 0.3545647 -9.651880 4.826276e-22 9.371019e-21 352 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199a-2'>Mir199a-2</a>
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138
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139 Mir182 Mir182 886.79583 4.919630 0.5101689 9.643140 5.255515e-22 9.996204e-21 7189 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a>
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140
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141 Snord91a Snord91a 168.95251 2.700421 0.2835464 9.523738 1.670595e-21 3.113990e-20 1437 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'>Snord91a</a>
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142
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143
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144 </pre>
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145
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146 <div class="toolFormTitle">Differential images and outputs</div>
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147 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
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148 <div><table class="simple" cellpadding="2" cellspacing="2">
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149 <tr>
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150 <td><a href="Differential_rowsum_bar_charts.pdf"><img src="Differential_rowsum_bar_charts.png" title="Click to download a PDF of Differential_rowsum_bar_charts.pdf" hspace="5" width="400"
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151 alt="Image called Differential_rowsum_bar_charts.pdf"/></a></td>
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152
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153 <td><a href="Differential_venn_edgeRtest_significant_genes_overlap.pdf"><img src="Differential_venn_edgeRtest_significant_genes_overlap.png" title="Click to download a PDF of Differential_venn_edgeRtest_significant_genes_overlap.pdf" hspace="5" width="400"
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154 alt="Image called Differential_venn_edgeRtest_significant_genes_overlap.pdf"/></a></td>
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155 </tr>
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156
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157 </table></div>
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158
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159 <div class="toolFormTitle">Differential log output</div>
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160
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161 <pre>
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162
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163 [1] @@@ Quantiles for non-zero row counts:
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164
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165 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
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166
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167 1.0 1.0 2.0 3.0 4.0 8.0 13.0 24.0 86.6 753.0 2325567.0
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168
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169 [1] Read 3242 contigs. Removed 1494 with no reads. After filtering at count quantile =0.3, there are 1141 contigs
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170
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171 [1] "@@ using genecards substitution for urls"
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172
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173 [1] @@ Total low count contigs per sample = 1,1,1,1,1,1,1,1
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174
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175 [1] Using samples: liver_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam,liver_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam,liver_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam,liver_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam,heart_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam,heart_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam,heart_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam,heart_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam
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176
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177 [1] Using design matrix:
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178
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179 (Intercept) groupliver
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180
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181 1 1 1
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182
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183 2 1 1
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184
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185 3 1 1
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186
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187 4 1 1
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188
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189 5 1 0
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190
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191 6 1 0
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192
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193 7 1 0
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194
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195 8 1 0
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196
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197 attr(,"assign")
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198
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199 [1] 0 1
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200
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201 attr(,"contrasts")
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202
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203 attr(,"contrasts")$group
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204
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205 [1] contr.treatment
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206
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207 [1] "Raw sample read totals 2443751,1644652,1682104,1806045,1440960,1341813,2888924,1428365"
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208
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209 [1] heart liver
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210
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211
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212 </pre>
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213
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214 <div class="toolFormTitle">Differential log output</div>
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215
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216 <pre>
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217
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218 Attaching package: ‘gplots’
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219
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220 The following object is masked from ‘package:stats’:
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221
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222 lowess
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223
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224 Loading required package: methods
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225
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226 Loading required package: limma
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227
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228 Loading required package: splines
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229
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230 Loading required package: DESeq2
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231
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232 Loading required package: GenomicRanges
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233
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234 Loading required package: BiocGenerics
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235
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236 Loading required package: parallel
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237
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238 Attaching package: ‘BiocGenerics’
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239
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111
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240 The following objects are masked from ‘package:parallel’:
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241
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242 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
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243
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244 The following object is masked from ‘package:limma’:
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245
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246 plotMA
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247
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248 The following object is masked from ‘package:stats’:
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249
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250 xtabs
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251
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252 The following objects are masked from ‘package:base’:
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253
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254 anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist
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255
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256 Loading required package: IRanges
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257
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258 Attaching package: ‘IRanges’
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259
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260 The following object is masked from ‘package:gplots’:
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261
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262 space
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263
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264 Loading required package: XVector
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265
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266 Loading required package: Rcpp
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267
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268 Loading required package: RcppArmadillo
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269
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270 gene-wise dispersion estimates
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271
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272 mean-dispersion relationship
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273
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274 final dispersion estimates
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275
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276 you had estimated gene-wise dispersions, removing these
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277
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278 you had estimated fitted dispersions, removing these
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279
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280 you had estimated gene-wise dispersions, removing these
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281
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282 you had estimated fitted dispersions, removing these
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283
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284 Warning message:
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285
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130
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286 closing unused connection 4 (edgeR.log)
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287
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288 Warning message:
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289
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290 In sink() : no sink to remove
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291
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292
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293 </pre>
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294
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295 <div class="toolFormTitle">VOOM images and outputs</div>
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296 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
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297 <div><table class="simple" cellpadding="2" cellspacing="2">
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298 <tr>
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130
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299 <td><a href="VOOM_edgeRtest_mean_variance_plot.pdf"><img src="VOOM_edgeRtest_mean_variance_plot.png" title="Click to download a PDF of VOOM_edgeRtest_mean_variance_plot.pdf" hspace="5" width="400"
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300 alt="Image called VOOM_edgeRtest_mean_variance_plot.pdf"/></a></td>
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301
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130
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302 <td><a href="VOOM_edgeRtest_qqplot.pdf"><img src="VOOM_edgeRtest_qqplot.png" title="Click to download a PDF of VOOM_edgeRtest_qqplot.pdf" hspace="5" width="400"
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303 alt="Image called VOOM_edgeRtest_qqplot.pdf"/></a></td>
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304 </tr>
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305
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306 </table></div>
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307
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308 <div class="toolFormTitle">VOOM log output</div>
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309
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310 <pre>
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311
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312 # VOOM top 50
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313
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130
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314 Contig logFC AveExpr t P.Value adj.P.Val B NReads URL
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315
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130
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316 Mir192 Mir192 6.689950 14.4417888 50.335160 1.802287e-16 2.056409e-13 27.414844 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
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317
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130
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318 Mir208a Mir208a -10.458438 3.8918506 -29.183545 2.249812e-13 1.283518e-10 19.141041 4638 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a>
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319
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320 Mir3073 Mir3073 8.318578 2.6485638 25.821264 1.102217e-12 4.192097e-10 18.063600 904 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a>
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25
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321
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130
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322 Mir802 Mir802 8.992449 2.9857711 25.195575 1.514327e-12 4.319618e-10 17.906674 1514 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
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25
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323
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130
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324 Mir208b Mir208b -12.256447 4.4678897 -22.360114 7.074494e-12 1.614400e-09 16.920424 14756 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
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25
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325
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326 Mir499 Mir499 -11.104485 3.8066799 -21.990054 8.769804e-12 1.667724e-09 16.728874 6527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
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25
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327
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130
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328 Mir10b Mir10b -4.775768 12.4173688 -21.487387 1.180685e-11 1.924516e-09 17.249348 197340 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
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25
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329
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130
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330 Mir148a Mir148a 2.751538 15.4237642 20.289553 2.464883e-11 3.515539e-09 16.455471 1002397 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'>Mir148a</a>
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25
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331
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130
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332 Mir490 Mir490 -8.497742 3.6613221 -18.336110 8.980482e-11 1.138526e-08 13.923237 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
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25
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333
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334 Mir122a Mir122a 10.197963 8.1512374 17.467826 1.663427e-10 1.897970e-08 14.215445 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
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25
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335
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130
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336 Mir133b Mir133b -6.172367 1.3497975 -17.274094 1.916064e-10 1.987481e-08 13.840201 159 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133b'>Mir133b</a>
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25
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337
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130
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338 Mir149 Mir149 -7.041176 6.0886889 -16.861286 2.602547e-10 2.474589e-08 13.714880 6164 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a>
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25
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339
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130
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340 Mir101b Mir101b 3.837883 10.6216725 15.443054 7.873164e-10 6.910215e-08 13.054350 59019 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
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25
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341
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130
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342 Mir143 Mir143 -1.912927 16.0353646 -14.922755 1.209475e-09 9.857220e-08 12.374988 1399819 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143'>Mir143</a>
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25
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343
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130
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344 Mir194-2 Mir194-2 5.534694 6.2627211 14.703097 1.455682e-09 1.107289e-07 12.316769 3570 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a>
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345
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130
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346 Mir23a Mir23a -2.905961 8.6431895 -14.558394 1.646894e-09 1.174441e-07 12.339306 10118 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a>
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347
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130
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348 Mir1983 Mir1983 -5.612359 1.1061384 -14.266537 2.119488e-09 1.422551e-07 11.743589 101 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1983'>Mir1983</a>
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349
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130
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350 Mir27a Mir27a -2.849084 10.0939084 -14.158498 2.329669e-09 1.476752e-07 11.960195 21886 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
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351
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130
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352 Cyp3a25 Cyp3a25 6.312461 1.6425308 13.845627 3.074630e-09 1.846396e-07 11.502713 226 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp3a25'>Cyp3a25</a>
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353
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354 Mir200a Mir200a 6.129125 1.8320913 13.226966 5.410979e-09 3.086963e-07 10.979834 264 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200a'>Mir200a</a>
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355
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130
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356 Mir181d Mir181d -3.405544 6.3702152 -13.064584 6.300369e-09 3.423201e-07 11.006301 2139 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a>
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357
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130
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358 Mir153 Mir153 -5.698257 1.5328802 -12.832092 7.856705e-09 3.829623e-07 10.583835 140 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir153'>Mir153</a>
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359
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130
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360 Mir204 Mir204 -7.718081 4.5031856 -12.808496 8.036265e-09 3.829623e-07 10.353229 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
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361
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130
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362 Gm5441 Gm5441 -5.716851 1.5430406 -12.806028 8.055298e-09 3.829623e-07 10.562881 142 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5441'>Gm5441</a>
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363
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364 Rabggtb Rabggtb 2.327908 9.9369857 12.760291 8.416902e-09 3.841474e-07 10.654006 19535 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
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365
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130
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366 Mir504 Mir504 -5.122304 0.8161671 -12.391521 1.205304e-08 5.289430e-07 10.144865 69 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir504'>Mir504</a>
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367
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368 Mir133a-1 Mir133a-1 -4.912497 0.7297882 -12.335045 1.274466e-08 5.385801e-07 10.076395 60 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133a-1'>Mir133a-1</a>
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369
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370 Mir195 Mir195 -2.954216 7.3530970 -12.081859 1.641098e-08 6.603731e-07 10.055879 3962 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a>
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371
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130
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372 Mir27b Mir27b -1.496991 14.9464877 -12.059553 1.678424e-08 6.603731e-07 9.674850 625308 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27b'>Mir27b</a>
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373
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130
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374 Snord52 Snord52 2.631712 9.7652181 11.922618 1.928407e-08 7.334374e-07 9.811774 18059 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord52'>Snord52</a>
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375
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130
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376 Mir322 Mir322 -3.029558 8.1188344 -11.736839 2.333148e-08 8.587488e-07 9.679815 7074 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a>
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377
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130
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378 Mir181c Mir181c -3.676262 9.6244506 -11.575598 2.758358e-08 9.835271e-07 9.453057 23605 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
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379
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130
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380 Mir1948 Mir1948 7.101780 4.7821564 11.471202 3.077353e-08 1.033009e-06 9.233632 2404 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a>
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381
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382 0610031O16Rik 0610031O16Rik 4.519875 0.7388871 11.470939 3.078205e-08 1.033009e-06 9.284014 78 <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610031O16Rik'>0610031O16Rik</a>
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383
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130
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384 Mir201 Mir201 -4.964105 0.7490919 -11.289794 3.729283e-08 1.210650e-06 9.114028 63 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir201'>Mir201</a>
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385
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130
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386 Mir21 Mir21 2.746616 13.2835800 11.267331 3.819755e-08 1.210650e-06 8.925217 229120 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
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387
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130
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388 Mir184 Mir184 -5.569565 2.3521173 -11.190343 4.148052e-08 1.279170e-06 8.854599 247 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a>
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389
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390 1810019D21Rik 1810019D21Rik 5.164581 1.0784751 11.082009 4.662057e-08 1.399844e-06 8.951908 117 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1810019D21Rik'>1810019D21Rik</a>
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391
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130
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392 Mir203 Mir203 2.216791 8.5426169 10.866758 5.896538e-08 1.725115e-06 8.715639 6739 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a>
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393
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130
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394 1110038B12Rik 1110038B12Rik 2.383720 10.6847245 10.832157 6.125623e-08 1.744094e-06 8.573067 37066 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1110038B12Rik'>1110038B12Rik</a>
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395
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396 Snord104 Snord104 2.571210 10.4798167 10.811468 6.267120e-08 1.744094e-06 8.561110 33458 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
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397
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130
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398 Mir182 Mir182 5.196800 7.2088299 10.640454 7.579543e-08 2.021320e-06 8.545839 7189 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a>
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399
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400 Mir547 Mir547 -4.542934 0.5799793 -10.635980 7.617593e-08 2.021320e-06 8.435473 42 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir547'>Mir547</a>
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401
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402 Mir143hg Mir143hg -2.291921 16.3789153 -10.597275 7.955395e-08 2.062978e-06 7.952584 1407364 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143hg'>Mir143hg</a>
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403
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130
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404 Scnn1b Scnn1b -4.541403 0.5700621 -10.243065 1.190487e-07 3.018546e-06 8.023327 45 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Scnn1b'>Scnn1b</a>
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405
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130
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406 Mir125b-2 Mir125b-2 -2.896115 7.2737925 -10.091091 1.420082e-07 3.522420e-06 7.876068 3837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a>
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407
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130
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408 Mir1a-1 Mir1a-1 -4.402568 0.4498447 -9.950346 1.675164e-07 4.066729e-06 7.692790 42 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1a-1'>Mir1a-1</a>
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25
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409
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130
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410 Mir378 Mir378 -2.733247 7.2964165 -9.922980 1.730212e-07 4.112858e-06 7.672216 4075 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a>
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411
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130
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412 Mir199b Mir199b -5.651345 2.8029895 -9.883978 1.812024e-07 4.219426e-06 7.548022 370 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a>
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413
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130
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414 Mir155 Mir155 -4.158272 3.8002361 -9.845490 1.896814e-07 4.328530e-06 7.604112 463 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a>
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415
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416
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417 </pre>
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418
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419 <div class="toolFormTitle">edgeR images and outputs</div>
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420 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
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421 <div><table class="simple" cellpadding="2" cellspacing="2">
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422 <tr>
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130
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423 <td><a href="edgeR_edgeRtest_BCV_vs_abundance.pdf"><img src="edgeR_edgeRtest_BCV_vs_abundance.png" title="Click to download a PDF of edgeR_edgeRtest_BCV_vs_abundance.pdf" hspace="5" width="400"
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424 alt="Image called edgeR_edgeRtest_BCV_vs_abundance.pdf"/></a></td>
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425
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426 <td><a href="edgeR_edgeRtest_GoodnessofFit.pdf"><img src="edgeR_edgeRtest_GoodnessofFit.png" title="Click to download a PDF of edgeR_edgeRtest_GoodnessofFit.pdf" hspace="5" width="400"
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427 alt="Image called edgeR_edgeRtest_GoodnessofFit.pdf"/></a></td>
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428
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429 <td><a href="edgeR_edgeRtest_MDSplot.pdf"><img src="edgeR_edgeRtest_MDSplot.png" title="Click to download a PDF of edgeR_edgeRtest_MDSplot.pdf" hspace="5" width="400"
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430 alt="Image called edgeR_edgeRtest_MDSplot.pdf"/></a></td>
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431 </tr>
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432 <tr>
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130
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433 <td><a href="edgeR_edgeRtest_qqplot.pdf"><img src="edgeR_edgeRtest_qqplot.png" title="Click to download a PDF of edgeR_edgeRtest_qqplot.pdf" hspace="5" width="400"
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434 alt="Image called edgeR_edgeRtest_qqplot.pdf"/></a></td>
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25
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435
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130
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436 <td><a href="edgeR_edgeRtest_smearplot.pdf"><img src="edgeR_edgeRtest_smearplot.png" title="Click to download a PDF of edgeR_edgeRtest_smearplot.pdf" hspace="5" width="400"
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437 alt="Image called edgeR_edgeRtest_smearplot.pdf"/></a></td>
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438
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439 <td><a href="edgeR_edgeRtest_top_100_heatmap.pdf"><img src="edgeR_edgeRtest_top_100_heatmap.png" title="Click to download a PDF of edgeR_edgeRtest_top_100_heatmap.pdf" hspace="5" width="400"
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440 alt="Image called edgeR_edgeRtest_top_100_heatmap.pdf"/></a></td>
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441 </tr>
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442
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130
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443 </table></div>
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444
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445 <div class="toolFormTitle">edgeR log output</div>
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446
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447 <pre>
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448
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449 [1] Common Dispersion = 0.228651460998105 CV = 0.478175136323613 getPriorN = 3.33333333333333
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25
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450
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451 [1] "No GLM fit outlier genes found\n"
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452
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130
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453 [1] @@ edgeR Top tags\n
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25
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454
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455 Name logFC logCPM LR PValue adj.p.value Dispersion totreads URL
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456
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457 Mir208a Mir208a -11.840751 8.465017 594.16946 3.104543e-131 3.542284e-128 0.05171220 4638 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a>
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458
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459 Mir149 Mir149 -7.008984 8.861767 484.30321 2.473909e-107 1.411365e-104 0.04959937 6164 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a>
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460
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130
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461 Mir208b Mir208b -13.291635 9.905945 417.69758 7.737463e-93 2.942815e-90 0.10508096 14756 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
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25
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462
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463 Mir122a Mir122a 10.514683 12.478088 415.17429 2.740525e-92 7.817349e-90 0.10803882 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
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464
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465 Mir204 Mir204 -7.498162 7.634507 341.30678 3.313430e-76 7.561247e-74 0.06907958 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
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25
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466
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130
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467 Mir499 Mir499 -13.577454 8.700078 325.79199 7.930755e-73 1.508165e-70 0.12042284 6527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
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25
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468
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130
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469 Mir490 Mir490 -8.534394 6.991023 303.17184 6.710366e-68 1.093790e-65 0.07949711 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
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25
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470
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130
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471 Mir192 Mir192 6.953853 17.169364 217.22867 3.638307e-49 5.189135e-47 0.12700995 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
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472
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130
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473 Mir802 Mir802 11.440805 6.593380 212.88059 3.231644e-48 4.097007e-46 0.12273671 1514 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
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25
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474
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475 Mir1948 Mir1948 7.418142 7.252734 195.66958 1.840248e-44 2.099723e-42 0.12060221 2404 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a>
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476
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477 Mir194-2 Mir194-2 5.298950 7.811522 191.85588 1.250960e-43 1.297587e-41 0.08670751 3570 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a>
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478
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479 Mir23a Mir23a -3.153807 9.529402 177.53185 1.676248e-40 1.593833e-38 0.04442763 10118 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a>
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480
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130
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481 Mir181c Mir181c -3.767686 10.639598 169.87390 7.883295e-39 6.919107e-37 0.06368883 23605 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
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25
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482
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130
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483 Mir3073 Mir3073 10.686337 5.859950 164.86740 9.778593e-38 7.969554e-36 0.14069249 904 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a>
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25
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484
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485 Mir181d Mir181d -3.643963 7.300371 162.18591 3.767663e-37 2.865936e-35 0.05729574 2139 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a>
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486
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487 Mir195 Mir195 -3.203683 8.215089 150.20548 1.563314e-34 1.114838e-32 0.05235020 3962 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a>
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488
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130
|
489 Mir10b Mir10b -5.182616 13.946466 147.24793 6.926819e-34 4.649118e-32 0.12268790 197340 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
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25
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490
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130
|
491 Mir101b Mir101b 3.759962 11.863187 136.31359 1.703812e-31 1.080028e-29 0.07961343 59019 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
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25
|
492
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|
493 Mir378 Mir378 -3.115599 8.119617 126.76408 2.092233e-29 1.256441e-27 0.05942391 4075 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a>
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494
|
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130
|
495 Mir27a Mir27a -3.064687 10.642480 124.98911 5.117477e-29 2.919520e-27 0.06113852 21886 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
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25
|
496
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|
497 Mir182 Mir182 5.057509 8.846381 123.17765 1.275060e-28 6.927826e-27 0.13653707 7189 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a>
|
|
|
498
|
|
|
499 Mir322 Mir322 -3.194159 9.012888 107.34926 3.732413e-25 1.935765e-23 0.07536483 7074 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a>
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|
|
500
|
|
|
501 Mir199b Mir199b -5.520119 4.792610 102.10724 5.259607e-24 2.609223e-22 0.13417024 370 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a>
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502
|
|
130
|
503 Mir181a-2 Mir181a-2 -3.000177 7.637692 101.38361 7.578821e-24 3.603098e-22 0.06896654 2817 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-2'>Mir181a-2</a>
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25
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504
|
|
|
505 Mir125b-2 Mir125b-2 -2.987759 8.144514 91.72544 9.957640e-22 4.488356e-20 0.07737381 3837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a>
|
|
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506
|
|
|
507 Dnm3os Dnm3os -3.331215 6.686950 91.67250 1.022763e-21 4.488356e-20 0.08810497 1401 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'>Dnm3os</a>
|
|
|
508
|
|
|
509 Mir184 Mir184 -5.111350 4.234160 84.35542 4.133639e-20 1.686711e-18 0.13502324 247 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a>
|
|
|
510
|
|
|
511 Mir215 Mir215 -3.058208 6.447966 84.35278 4.139167e-20 1.686711e-18 0.08138517 1182 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'>Mir215</a>
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512
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130
|
513 Mir133b Mir133b -8.383611 3.584760 83.96681 5.031517e-20 1.960318e-18 0.17482280 159 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133b'>Mir133b</a>
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25
|
514
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130
|
515 Mir150 Mir150 -2.883446 8.307765 83.91918 5.154210e-20 1.960318e-18 0.08008123 4229 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir150'>Mir150</a>
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25
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516
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|
517 Mir3074-2 Mir3074-2 -2.778308 7.935651 83.74839 5.619282e-20 2.040616e-18 0.07424646 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'>Mir3074-2</a>
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518
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130
|
519 Mir24-2 Mir24-2 -2.778307 7.935651 83.71222 5.723024e-20 2.040616e-18 0.07427992 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'>Mir24-2</a>
|
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25
|
520
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|
|
521 Mir193 Mir193 5.176579 4.801090 83.19222 7.445011e-20 2.574169e-18 0.14794861 421 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193'>Mir193</a>
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|
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522
|
|
|
523 Scarna17 Scarna17 2.182159 9.244479 81.91330 1.421894e-19 4.771710e-18 0.04982909 9224 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Scarna17'>Scarna17</a>
|
|
|
524
|
|
130
|
525 Mir214 Mir214 -3.271172 6.271755 80.43948 2.997458e-19 9.771712e-18 0.09566584 1048 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a>
|
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25
|
526
|
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130
|
527 Snord104 Snord104 2.330488 11.053611 79.50529 4.809369e-19 1.524303e-17 0.05915990 33458 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
|
|
25
|
528
|
|
|
529 Mir200a Mir200a 7.201555 4.139422 77.35503 1.428304e-18 4.365755e-17 0.19287764 264 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200a'>Mir200a</a>
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|
|
530
|
|
|
531 Mir200b Mir200b 6.525423 5.752604 77.31985 1.453976e-18 4.365755e-17 0.26237966 888 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200b'>Mir200b</a>
|
|
|
532
|
|
130
|
533 Mir21 Mir21 2.923147 13.825255 75.51798 3.620938e-18 1.059357e-16 0.09395834 229120 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
|
|
25
|
534
|
|
|
535 Mir203 Mir203 1.956427 8.767610 75.17870 4.299815e-18 1.226522e-16 0.04381710 6739 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a>
|
|
|
536
|
|
|
537 Mir155 Mir155 -3.886731 5.068563 73.81316 8.587210e-18 2.389758e-16 0.12522673 463 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a>
|
|
|
538
|
|
130
|
539 Cyp3a25 Cyp3a25 8.681501 3.972085 72.29680 1.851471e-17 5.029829e-16 0.23125383 226 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp3a25'>Cyp3a25</a>
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25
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540
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130
|
541 Rabggtb Rabggtb 1.934093 10.298211 72.02043 2.129809e-17 5.651422e-16 0.04596646 19535 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
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25
|
542
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|
130
|
543 Mir23b Mir23b -2.100584 10.184110 71.44225 2.854935e-17 7.403367e-16 0.05416378 16387 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a>
|
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25
|
544
|
|
130
|
545 Snord52 Snord52 2.207491 10.217554 71.27974 3.100027e-17 7.860292e-16 0.05941483 18059 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord52'>Snord52</a>
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25
|
546
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130
|
547 Gm5441 Gm5441 -6.881248 3.538457 70.05615 5.764004e-17 1.429724e-15 0.20097284 142 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5441'>Gm5441</a>
|
|
25
|
548
|
|
130
|
549 Mir153 Mir153 -6.857671 3.517446 69.37600 8.137282e-17 1.975455e-15 0.20158808 140 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir153'>Mir153</a>
|
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25
|
550
|
|
|
551 Mir132 Mir132 -2.858294 5.938312 64.52507 9.531204e-16 2.265647e-14 0.09274248 857 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'>Mir132</a>
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|
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552
|
|
|
553 1110038B12Rik 1110038B12Rik 2.195962 11.253090 62.92015 2.152583e-15 5.012443e-14 0.06712174 37066 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1110038B12Rik'>1110038B12Rik</a>
|
|
|
554
|
|
|
555 Snord91a Snord91a 2.654072 6.557504 62.40549 2.795431e-15 6.379174e-14 0.08637410 1437 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'>Snord91a</a>
|
|
|
556
|
|
130
|
557 [1] @@ 416 tags significant at adj p= 0.05
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25
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558
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|
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559
|
|
|
560 </pre>
|
|
|
561
|
|
|
562 <div class="toolFormTitle">Other log output</div>
|
|
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563
|
|
|
564 <pre>
|
|
|
565
|
|
|
566 ## Toolfactory generated command line = Rscript - None None
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567
|
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568 Got TCols=1 5 6 7; CCols=2 3 4 8
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569
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130
|
570 R version 3.0.2 (2013-09-25)
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25
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571
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130
|
572 Platform: x86_64-pc-linux-gnu (64-bit)
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25
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573
|
|
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574 locale:
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575
|
|
111
|
576 [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 LC_PAPER=en_AU.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
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25
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577
|
|
|
578 attached base packages:
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579
|
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111
|
580 [1] parallel splines methods stats graphics grDevices utils datasets base
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25
|
581
|
|
|
582 other attached packages:
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|
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583
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130
|
584 [1] RColorBrewer_1.0-5 DESeq2_1.2.10 RcppArmadillo_0.4.400.0 Rcpp_0.11.2 GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.7 BiocGenerics_0.8.0 edgeR_3.4.2 limma_3.18.13 gplots_2.15.0 stringr_0.6.2
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25
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585
|
|
|
586 loaded via a namespace (and not attached):
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|
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587
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|
130
|
588 [1] annotate_1.40.1 AnnotationDbi_1.24.0 Biobase_2.22.0 bitops_1.0-6 caTools_1.17.1 DBI_0.3.0 gdata_2.13.3 genefilter_1.44.0 grid_3.0.2 gtools_3.4.1 KernSmooth_2.23-13 lattice_0.20-29 locfit_1.5-9.1 RSQLite_0.11.4 stats4_3.0.2 survival_2.37-7 XML_3.98-1.1 xtable_1.7-4
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25
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589
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|
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590
|
|
|
591 </pre>
|
|
|
592
|
|
|
593 <div class="toolFormTitle">All output files available for downloading</div>
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|
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594
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595 <div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>
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596
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111
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597 <tr><td><a href="DESeq2.log">DESeq2.log</a></td><td>10.5 KB</td></tr>
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130
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598 <tr class="odd_row"><td><a href="DESeq2_edgeRtest_MA_plot.pdf">DESeq2_edgeRtest_MA_plot.pdf</a></td><td>15.0 KB</td></tr>
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599 <tr><td><a href="DESeq2_edgeRtest_PCA_plot.pdf">DESeq2_edgeRtest_PCA_plot.pdf</a></td><td>4.9 KB</td></tr>
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600 <tr class="odd_row"><td><a href="DESeq2_edgeRtest_dispersion_estimates.pdf">DESeq2_edgeRtest_dispersion_estimates.pdf</a></td><td>190.6 KB</td></tr>
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601 <tr><td><a href="DESeq2_edgeRtest_qqplot.pdf">DESeq2_edgeRtest_qqplot.pdf</a></td><td>13.3 KB</td></tr>
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602 <tr class="odd_row"><td><a href="DESeq2_edgeRtest_sample_distance_plot.pdf">DESeq2_edgeRtest_sample_distance_plot.pdf</a></td><td>9.5 KB</td></tr>
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603 <tr><td><a href="Differential.log">Differential.log</a></td><td>1.4 KB</td></tr>
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604 <tr class="odd_row"><td><a href="Differential_Counts.Rscript">Differential_Counts.Rscript</a></td><td>28.3 KB</td></tr>
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605 <tr><td><a href="Differential_Counts_error.log">Differential_Counts_error.log</a></td><td>1.8 KB</td></tr>
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606 <tr class="odd_row"><td><a href="Differential_Counts_runner.log">Differential_Counts_runner.log</a></td><td>1.3 KB</td></tr>
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607 <tr><td><a href="Differential_rowsum_bar_charts.pdf">Differential_rowsum_bar_charts.pdf</a></td><td>6.3 KB</td></tr>
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608 <tr class="odd_row"><td><a href="Differential_venn_edgeRtest_significant_genes_overlap.pdf">Differential_venn_edgeRtest_significant_genes_overlap.pdf</a></td><td>9.7 KB</td></tr>
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609 <tr><td><a href="VOOM.log">VOOM.log</a></td><td>10.1 KB</td></tr>
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610 <tr class="odd_row"><td><a href="VOOM_edgeRtest_mean_variance_plot.pdf">VOOM_edgeRtest_mean_variance_plot.pdf</a></td><td>18.3 KB</td></tr>
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611 <tr><td><a href="VOOM_edgeRtest_qqplot.pdf">VOOM_edgeRtest_qqplot.pdf</a></td><td>17.5 KB</td></tr>
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612 <tr class="odd_row"><td><a href="edgeR.log">edgeR.log</a></td><td>10.4 KB</td></tr>
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613 <tr><td><a href="edgeR_edgeRtest_BCV_vs_abundance.pdf">edgeR_edgeRtest_BCV_vs_abundance.pdf</a></td><td>17.4 KB</td></tr>
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614 <tr class="odd_row"><td><a href="edgeR_edgeRtest_GoodnessofFit.pdf">edgeR_edgeRtest_GoodnessofFit.pdf</a></td><td>13.1 KB</td></tr>
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615 <tr><td><a href="edgeR_edgeRtest_MDSplot.pdf">edgeR_edgeRtest_MDSplot.pdf</a></td><td>4.9 KB</td></tr>
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616 <tr class="odd_row"><td><a href="edgeR_edgeRtest_qqplot.pdf">edgeR_edgeRtest_qqplot.pdf</a></td><td>15.2 KB</td></tr>
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617 <tr><td><a href="edgeR_edgeRtest_smearplot.pdf">edgeR_edgeRtest_smearplot.pdf</a></td><td>16.7 KB</td></tr>
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618 <tr class="odd_row"><td><a href="edgeR_edgeRtest_top_100_heatmap.pdf">edgeR_edgeRtest_top_100_heatmap.pdf</a></td><td>11.2 KB</td></tr>
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25
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619 </table></div><br/>
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620 </div></body></html>
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621
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