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1 <tool id="sartools_deseq2" name="SARTools DESeq2" version="@WRAPPER_VERSION@.0">
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2
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3 <!-- [REQUIRED] Tool description displayed after the tool name -->
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4 <description>Compare two or more biological conditions in a RNA-Seq framework with DESeq2</description>
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5
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12
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13 <!-- [REQUIRED] The command to execute -->
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14 <command interpreter="python"><![CDATA[
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15
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16 abims_sartools_deseq2_wrapper.py
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17 ## parameters
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18 @COMMAND_BASIC_PARAMETERS@
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19 #if str( $advanced_parameters.adv_param ) == "show":
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20 @COMMAND_BATCH_PARAM@
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21 --fitType $advanced_parameters.fitType
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22 --cooksCutoff $advanced_parameters.cooksCutoff
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23 --independentFiltering $advanced_parameters.independentFiltering
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24 --alpha $advanced_parameters.alpha
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25 --pAdjustMethod $advanced_parameters.pAdjustMethod
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26 --typeTrans $advanced_parameters.typeTrans
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27 --locfunc $advanced_parameters.locfunc
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28 --colors $advanced_parameters.colors
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29 --forceCairoGraph $advanced_parameters.forceCairoGraph
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30 #end if
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31 ## ouputs
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32 @COMMAND_OUTPUTS@
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33
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34 ]]></command>
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35
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36 <!-- [REQUIRED] Input files and tool parameters -->
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37 <inputs>
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38
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39 <expand macro="basic_parameters" />
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40
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41 <conditional name="advanced_parameters" >
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42 <param name="adv_param" type="select" label="Advanced Parameters" help="" >
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43 <option value="hide" selected="true">Hide</option>
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44 <option value="show">Show</option>
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45 </param>
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46 <when value="hide" />
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47 <when value="show">
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48 <expand macro="batch_param" />
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49 <param type="select" label="Mean-variance relationship" argument="--fitType" help="Type of model for the mean-dispersion relationship. Parametric by default." >
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50 <option value="parametric" selected="true">parametric</option>
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51 <option value="local">local</option>
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3
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52 <option value="mean">mean</option>
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53 </param>
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54 <param type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform the outliers detection" argument="--cooksCutoff" help="Checked by default."/>
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55 <param type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform independent filtering" argument="--independentFiltering" help="Checked by default."/>
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56 <expand macro="alpha_param" />
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57 <expand macro="padjustmethod_param" />
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58 <param type="select" label="Transformation for PCA/clustering" argument="--typeTrans" help="Method of transformation of the counts for the clustering and the PCA: 'VST' (default) for Variance Stabilizing Transformation, or 'rlog' for Regularized Log Transformation." >
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59 <option value="VST" selected="true">VST</option>
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60 <option value="rlog">rlog</option>
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61 </param>
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62 <param type="select" label="Estimation of the size factors" argument="--locfunc" help="'median' (default) or 'shorth' from the genefilter package." >
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63 <option value="median" selected="true">median</option>
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64 <option value="shorth">shorth</option>
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65 </param>
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66 <expand macro="colors_param" />
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67 <expand macro="forceCairoGraph_param" />
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68 </when>
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69 </conditional>
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70
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71 </inputs>
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72
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73 <!-- [REQUIRED] Output files -->
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74 <outputs>
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75
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76 <expand macro="outputs" />
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77
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78 </outputs>
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79
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80 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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81 <tests>
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82 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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83 <test>
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84 <!-- Test with 2 conditions, 2 replicates, 8217 features -->
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85 <param name="targetFile" dbkey="?" value="target.txt" />
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86 <param name="rawDir" value="raw.zip" dbkey="?" ftype="zip"/>
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87 <param name="adv_param" value="show"/>
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88 <output name="log">
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89 <assert_contents>
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90 <has_text text="KO vs WT 0.1 171" />
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3
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91 <has_text text="KO vs WT 2583 2663 5246" />
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92 <has_text text="HTML report created" />
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93 </assert_contents>
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94 </output>
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95 </test>
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96 <!-- <test>
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97 --> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10160 features, with batch effect -->
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98 <!-- <param name="targetFile" dbkey="?" value="targetT048.txt" />
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99 <param name="rawDir" value="rawT048.zip" dbkey="?" ftype="no_unzip.zip"/>
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100 <param name="condRef" value="T0"/>
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101 <param name="adv_param" value="show"/>
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102 <param name="condition" value="true"/>
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103 <output name="tables_html" file="SARTools_DESeq2_targetT048_tables.html" lines_diff="14">
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104 <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_DESeq2_T4vsT0.complete.txt"/>
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105 <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_DESeq2_T8vsT0.complete.txt"/>
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106 <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_DESeq2_T8vsT4.complete.txt"/>
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107 </output>
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108 </test>
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109 --> </tests>
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110
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111 <!-- [OPTIONAL] Help displayed in Galaxy -->
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112 <help><![CDATA[
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113
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114 @HELP_AUTHORS@
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115
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116 ===============
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117 SARTools DESeq2
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118 ===============
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119
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120 -----------
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121 Description
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122 -----------
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123
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124 @HELP_DESCRIPTION@
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125
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126
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127 -----------
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128 Input files
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129 -----------
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130
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131 @HELP_INPUT_FILES@
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132
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133
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134 ----------
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135 Parameters
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136 ----------
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137
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138 @HELP_BASIC_PARAMETERS@
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139 * **batch:** adjustment variable to use as a batch effect, must be a column of the target file (NULL if no batch effect needs to be taken into account);
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140 * **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05);
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141 * **fitType:** type of model for the mean-dispersion relationship ("parametric" by default, or "local");
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142 * **cooksCutoff:** TRUE (default) of FALSE to execute or not the detection of the outliers [4];
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143 * **independentFiltering:** TRUE (default) of FALSE to execute or not the independent filtering [5];
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144 * **pAdjustMethod:** p-value adjustment method for multiple testing [6, 7] ("BH" by default, "BY" or any value of p.adjust.methods);
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145 * **typeTrans:** method of transformation of the counts for the clustering and the PCA (default is "VST" for Variance Stabilizing Transformation, or "rlog" for Regularized Log Transformation);
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146 * **locfunc:** function used for the estimation of the size factors (default is "median", or "shorth" from the genefilter package);
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147 * **colors:** colors used for the figures (one per biological condition), 8 are given by default.
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3
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148 * **forceCairoGraph:** TRUE or FALSE (default) to force the use of cairo with options(bitmapType="cairo").
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149
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150
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151 ------------
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152 Output files
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153 ------------
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154
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155 @HELP_OUTPUT_FILES@
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156
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157
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158 ---------------------------------------------------
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159
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160 [1] G.-K. Smyth. Limma: linear models for microarray data. In R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, and W. Huber, editors, Bioinformatics and Computational Biology Solutions Using R and Bioconductor, pages 397–420. Springer, New York, 2005.
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161
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162 [2] S. Anders. HTSeq: Analysing high-throughput sequencing data with Python. http://www-huber.embl.de/users/anders/HTSeq/, 2011.
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163
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164 [3] S. Anders, P.-T. Pyl, and W. Huber. HTSeq - A Python framework to work with high-throughput sequencing data. bioRxiv preprint, 2014. URL: http://dx.doi.org/10.1101/002824.
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165
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166 [4] R.-D. Cook. Detection of Influential Observation in Linear Regression. Technometrics, February 1977.
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167
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168 [5] R. Bourgon, R. Gentleman, and W. Huber. Independent filtering increases detection power for high-throughput experiments. PNAS, 107(21):9546–9551, 2010. URL: http://www.pnas.org/content/107/21/9546.long.
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169
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170 [6] Y. Benjamini and Y. Hochberg. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B, 57:289–300, 1995.
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171
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172 [7] Y. Benjamini and D. Yekutieli. The control of the false discovery rate in multiple testing under dependency. Ann. Statist., 29(4):1165–1188, 2001.
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173
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174
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175 ]]></help>
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176
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177 <citations>
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178 <expand macro="common_citations" />
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179 <citation type="bibtex">@ARTICLE{Cook77,
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180 author = {R.-D. Cook},
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181 title = {Detection of Influential Observation in Linear Regression},
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182 journal = {Technometrics},
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183 year = {1977},
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184 month = {February}
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185 }</citation>
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186 <citation type="bibtex">@ARTICLE{Bourgon10,
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187 author = {R. Bourgon, R. Gentleman, and W. Huber},
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188 title = {Independent filtering increases detection power for high-throughput experiments},
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189 journal = {PNAS},
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190 year = {2010},
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191 volume = {107},
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192 number = {21},
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193 pages = {9546–9551},
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194 note = {URL: http://www.pnas.org/content/107/21/9546.long}
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195 }</citation>
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196 </citations>
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197
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198 </tool>
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