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1 <tool id="sartools_edger" name="SARTools edgeR" version="1.0.0">
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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 edgeR</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
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14 <!-- [REQUIRED] The command to execute -->
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15 <command interpreter="python"><![CDATA[
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16
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17 abims_sartools_edger_wrapper.py
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18 ## parameters
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19 @COMMAND_BASIC_PARAMETERS@
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20 #if str( $advanced_parameters.adv_param ) == "show":
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21 @COMMAND_BATCH_PARAM@
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22 --alpha $advanced_parameters.alpha
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23 --pAdjustMethod $advanced_parameters.pAdjustMethod
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24 --cpmCutoff $advanced_parameters.cpmCutoff
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25 --geneSelection $advanced_parameters.geneSelection
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26 --normalizationMethod $advanced_parameters.normalizationMethod
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27 --colors $advanced_parameters.colors
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28 #end if
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29 ## ouputs
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30 @COMMAND_OUTPUTS@
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31
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32 ]]></command>
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33
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34 <!-- [REQUIRED] Input files and tool parameters -->
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35 <inputs>
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36
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37 <expand macro="basic_parameters" />
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38
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39 <conditional name="advanced_parameters" >
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40 <param name="adv_param" type="select" label="Advanced Parameters" help="" >
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41 <option value="hide" selected="true">Hide</option>
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42 <option value="show">Show</option>
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43 </param>
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44 <when value="hide" />
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45 <when value="show">
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46 <expand macro="batch_param" />
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47 <expand macro="alpha_param" />
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48 <expand macro="padjustmethod_param" />
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49 <param name="cpmCutoff" type="integer" value="1" min="0" label="Counts-per-million cut-off to filter low counts" help="(-m, --cpmCutoff) Set to 0 to disable filtering. Default is 1." />
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50 <param name="geneSelection" type="select" label="Selection of the features in MDSPlot" help="(-g, --gene.selection) Default is 'pairwise'." >
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51 <option value="pairwise" selected="true">pairwise</option>
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52 <option value="common">common</option>
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53 </param>
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54 <param name="normalizationMethod" type="select" label="Normalization method in calcNormFactors" help="(-n, --normalizationMethod) 'TMM' (default), 'RLE' (DESeq method) or 'upperquartile'." >
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55 <option value="TMM" selected="true">TMM</option>
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56 <option value="RLE">RLE</option>
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57 <option value="upperquartile">upperquartile</option>
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58 </param>
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59 <expand macro="colors_param" />
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60 </when>
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61 </conditional>
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62
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63 </inputs>
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64
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65 <!-- [REQUIRED] Output files -->
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66 <outputs>
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67
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68 <expand macro="outputs" />
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69
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70 </outputs>
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71
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72 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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73 <tests>
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74 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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75 <test>
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76 <!-- Test with 2 conditions, 2 replicates, 10 features -->
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77 <param name="targetFile" dbkey="?" value="target_small.txt" />
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78 <param name="rawDir" value="raw_small.zip" dbkey="?" ftype="zip"/>
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79 <param name="adv_param" value="show"/>
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80 <output name="log">
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81 <assert_contents>
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82 <has_text text="KO vs WT 5 4 9" />
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83 <has_text text="HTML report created" />
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84 </assert_contents>
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85 </output>
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86 </test>
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87 <!-- <test>
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88 --> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10 features, with batch effect -->
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89 <!-- <param name="targetFile" dbkey="?" value="targetT048_small.txt" />
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90 <param name="rawDir" value="rawT048_small.zip" dbkey="?" ftype="no_unzip.zip"/>
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91 <param name="condRef" value="T0"/>
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92 <param name="adv_param" value="show"/>
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93 <param name="condition" value="true"/>
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94 <output name="tables_html" file="SARTools_edgeR_targetT048_small_tables.html" lines_diff="12">
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95 <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0_small.complete.txt"/>
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96 <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0_small.complete.txt"/>
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97 <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4_small.complete.txt"/>
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98 </output>
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99 </test>
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100 --> <test>
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101 <!-- Test with 2 conditions, 2 replicates, 8217 features -->
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102 <param name="targetFile" dbkey="?" value="target.txt" />
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103 <param name="rawDir" value="raw.zip" dbkey="?" ftype="zip"/>
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104 <param name="adv_param" value="show"/>
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105 <output name="log">
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106 <assert_contents>
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107 <has_text text="KO vs WT 2691 2713 5404" />
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108 <has_text text="HTML report created" />
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109 </assert_contents>
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110 </output>
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111 </test>
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112 <!-- <test>
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113 --> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10160 features, with batch effect -->
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114 <!-- <param name="targetFile" dbkey="?" value="targetT048.txt" />
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115 <param name="rawDir" value="rawT048.zip" dbkey="?" ftype="no_unzip.zip"/>
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116 <param name="condRef" value="T0"/>
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117 <param name="adv_param" value="show"/>
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118 <param name="condition" value="true"/>
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119 <output name="tables_html" file="SARTools_edgeR_targetT048_tables.html" lines_diff="14">
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120 <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0.complete.txt"/>
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121 <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0.complete.txt"/>
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122 <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4.complete.txt"/>
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123 </output>
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124 </test>
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125 --> </tests>
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126
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127 <!-- [OPTIONAL] Help displayed in Galaxy -->
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128 <help><![CDATA[
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129
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130 @HELP_AUTHORS@
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131
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132 ==============
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133 SARTools edgeR
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134 ==============
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135
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136 -----------
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137 Description
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138 -----------
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139
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140 @HELP_DESCRIPTION@
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141
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142
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143 -----------
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144 Input files
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145 -----------
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146
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147 @HELP_INPUT_FILES@
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148
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149
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150 ----------
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151 Parameters
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152 ----------
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153
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154 @HELP_BASIC_PARAMETERS@
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155 * **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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156 * **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05);
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157 * **pAdjustMethod:** p-value adjustment method for multiple testing [4, 5] ("BH" by default, "BY" or any value of p.adjust.methods);
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158 * **cpmCutoff:** counts-per-million cut-off to filter low counts (default is 1, set to 0 to disable filtering);
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159 * **gene.selection:** method of selection of the features for the MultiDimensional Scaling plot ("pairwise" by default or common);
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160 * **normalizationMethod:** normalization method in calcNormFactors(): "TMM" (default), "RLE" (DESeq method) or "upperquartile";
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161 * **colors:** colors used for the figures (one per biological condition), 8 are given by default.
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162
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163
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164 ------------
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165 Output files
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166 ------------
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167
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168 @HELP_OUTPUT_FILES@
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169
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170
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171 ---------------------------------------------------
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172
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173 [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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174
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175 [2] S. Anders. HTSeq: Analysing high-throughput sequencing data with Python. http://www-huber.embl.de/users/anders/HTSeq/, 2011.
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176
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177 [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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178
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179 [4] 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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180
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181 [5] 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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182
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183
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184 ]]></help>
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185
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186 <citations>
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187 <expand macro="common_citations" />
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188 </citations>
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189
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190 </tool>
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