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annotate quantp.xml @ 3:a8bedebab467 draft default tip

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planemo upload commit 30548b09c6490f2f1f4d953a54c114d8e895fb5a
author galaxyp
date Wed, 06 Feb 2019 11:35:44 -0500
parents ed0bb50d7ffe
children
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1 <tool id="quantp" name="QuanTP" version="1.1.2">
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2 <description>Correlation between protein and transcript abundances</description>
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3 <requirements>
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4 <requirement type="package" version="1.10.4">r-data.table</requirement>
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5 <requirement type="package" version="3.0.1">r-gplots</requirement>
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6 <requirement type="package" version="0.7.6">r-dplyr</requirement>
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7 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
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8 <requirement type="package" version="0.4.5">r-ggfortify</requirement>
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9 <requirement type="package" version="4.8.0">r-plotly</requirement>
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10 <requirement type="package" version="0.6.1.1">r-d3heatmap</requirement>
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11 <requirement type="package" version="0.5.0">r-munsell</requirement>
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12 </requirements>
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13 <command detect_errors="exit_code"><![CDATA[
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14 Rscript '$__tool_directory__/quantp.r'
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15 $experiment_design_option.sample_type
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16 $experiment_design_option.method_type
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17 $experiment_design_option.exp_design
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18 '$pe_exp'
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19 '$te_exp'
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20 $experiment_design_option.correction_method
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21 $cooksd_upper
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22 $nclust
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23 $hm_nclust
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24 $experiment_design_option.volcano_with
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25 '$html_file'
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26 '$html_file.files_path'
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27 ]]></command>
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28 <inputs>
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29 <param name="pe_exp" type="data" format="tabular" label="Input Protein Abundance File" help="Protein abundance input file"/>
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30 <param name="te_exp" type="data" format="tabular" label="Input RNA Abundance File" help="Transcript abundance input file"/>
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31 <conditional name="experiment_design_option">
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32 <param name="sample_type" type="select" label="Select data input type" help="If the input files already have fold-change values, select Log fold-change. Else, select abundances and the tool will perform the fold-change analysis">
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33 <option value="multiple" selected="True">Abundances from different conditions with or without replicates (in multiple columns)</option>
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34 <option value="logfold">Log fold-change values (or single condition abundance without replicates in single column) data</option>
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35 </param>
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36 <when value="logfold">
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37 <param name="exp_design" type="hidden" value="none" />
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38 <param name="method_type" type="hidden" value="none" />
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39 <param name="correction_method" type="hidden" value="none" />
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40 <param name="volcano_with" type="hidden" value="pval" />
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41 </when>
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42 <when value="multiple">
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43 <param name="exp_design" type="data" format="tabular" help="Please check the format of the experiment design file">
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44 <label>Experiment design File (Please see the format below)</label>
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45 </param>
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46 <param name="method_type" type="select" label="Data summarization method" help="Perform T-Test on selecting Mean; Wilcoxon Ranksum Test on selecting Median">
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47 <option value="mean" selected="True">Mean (Default)</option>
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48 <option value="median">Median</option>
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49 </param>
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50 <param name="correction_method" type="select" label="Multiple testing correction method">
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51 <option value="BH" selected="True">Benjamini and Hochberg (BH) (Default)</option>
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52 <option value="holm">Holm</option>
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53 <option value="hochberg">Hochberg</option>
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54 <option value="hommel">Hommel</option>
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55 <option value="bonferroni">Bonferroni</option>
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56 <option value="BY">Benjamini and Yekutieli (BY)</option>
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57 <option value="none">None</option>
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58 </param>
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59 <param name="volcano_with" type="select" display="radio" label="Volcano plot with p-value or adjusted p-value">
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60 <option value="pval" selected="True">P-value (Default)</option>
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61 <option value="adj_pval">Adjusted P-value</option>
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62 </param>
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63 </when>
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64 </conditional>
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65 <param name="cooksd_upper" type="integer" value="4" optional="false" >
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66 <label>Influential Observation cutoff: Observations > value * mean of Cook's distances (Default: "4" * mean(Cook's Distance))</label>
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67 </param>
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68 <param name="nclust" type="select" label="K-mean clustering: Number of clusters">
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69 <option value="1">1</option>
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70 <option value="2">2</option>
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71 <option value="3">3</option>
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72 <option value="4" selected="True">4</option>
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73 <option value="5">5</option>
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74 <option value="6">6</option>
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75 <option value="7">7</option>
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76 <option value="8">8</option>
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77 <option value="9">9</option>
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78 <option value="10">10</option>
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79 </param>
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80
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81 <param name="hm_nclust" type="select" label="Hierarchical clustering: Number of clusters (from Heatmap)">
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82 <option value="1">1</option>
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83 <option value="2">2</option>
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84 <option value="3">3</option>
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85 <option value="4">4</option>
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86 <option value="5" selected="True">5</option>
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87 <option value="6">6</option>
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88 <option value="7">7</option>
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89 <option value="8">8</option>
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90 <option value="9">9</option>
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91 <option value="10">10</option>
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92 </param>
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93 </inputs>
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94 <outputs>
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95 <data format="html" name="html_file" label="protein transcript correlation on ${pe_exp.name} and ${te_exp.name}"/>
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96 </outputs>
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97 <tests>
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98 <test>
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99 <conditional name="experiment_design_option">
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100 <param name="sample_type" value="multiple"/>
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101 <param name="method_type" value="mean"/>
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102 <param name="exp_design" value="exp_design_file.tabular" ftype="tabular" />
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103 <param name="correction_method" value="BH"/>
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104 <param name="volcano_with" value="pval"/>
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105 </conditional>
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106 <param name="pe_exp" value="protein_data.tabular" ftype="tabular" />
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107 <param name="te_exp" value="transcript_data.tabular" ftype="tabular" />
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108 <param name="cooksd_upper" value="4"/>
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109 <param name="nclust" value="4"/>
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110 <param name="hm_nclust" value="5"/>
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111 <output name="html_file">
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112 <assert_contents>
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113 <has_text text="SAMPLE DISTRIBUTION" />
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114 <has_text text="plotly" />
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115 </assert_contents>
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116 </output>
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117 </test>
2
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118 <test>
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119 <conditional name="experiment_design_option">
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120 <param name="sample_type" value="logfold"/>
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121 <param name="correction_method" value="BH"/>
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122 <param name="volcano_with" value="pval"/>
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123 </conditional>
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124 <param name="pe_exp" value="mouse_protein_log_data.txt" ftype="tabular" />
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125 <param name="te_exp" value="mouse_transcript_log_data.txt" ftype="tabular" />
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126 <param name="cooksd_upper" value="4"/>
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127 <param name="nclust" value="4"/>
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128 <param name="hm_nclust" value="5"/>
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129 <output name="html_file">
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130 <assert_contents>
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131 <has_text text="SAMPLE DISTRIBUTION" />
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132 <has_text text="plotly" />
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133 </assert_contents>
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134 </output>
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135 </test>
0
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136 </tests>
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137 <help><![CDATA[
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138
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139 **What it does**
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140
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141 QuanTP correlates *transcript abundance* and *protein abundance* to examine the association between them.
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142
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143 It either takes in the log fold-change of abundances as input or raw abundances from different conditions where it calculates the log ratios of abundances between two conditions.
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144
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145 Transcript input file can be generated from the quantitative RNA-Seq study whereas Protein input file can be generated from quantitative analysis of mass-spectrometry-based protein data.
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146
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147 -----
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148
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149 **Input file formats**
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150
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151 **Protein data file**
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152
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153 First column - Gene
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154
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155 Following columns - Abundance values (or log fold-change values)
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156
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157 Example of Protein input file
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158
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159 ====== ========= ========= ========= ========= ========= ========= ========= =========
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160 Gene sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8
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161 ------ --------- --------- --------- --------- --------- --------- --------- ---------
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162 GeneX value value value value value value value value
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163 GeneY value value value value value value value value
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164 GeneZ value value value value value value value value
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165 ====== ========= ========= ========= ========= ========= ========= ========= =========
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166
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167
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168 **Transcript data file**
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169
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170 First column - Gene
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171
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172 Following columns - Abundance values (or log fold-change values)
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173
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174 Example of Transcript input file
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175
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176 ====== ========= ========= ========= ========= ========= ========= ========= =========
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177 Gene sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8
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178 ------ --------- --------- --------- --------- --------- --------- --------- ---------
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179 GeneX value value value value value value value value
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180 GeneY value value value value value value value value
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181 GeneZ value value value value value value value value
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182 ====== ========= ========= ========= ========= ========= ========= ========= =========
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183
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184
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185 **Data input type**
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186
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187 If data input type is abundance, experiment design file is required.
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188
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189 Example of experiment design file
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190
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191 ======== =========
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192 case groupA
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193 control groupB
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194 sample1 groupA
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195 sample2 groupA
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196 sample3 groupA
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197 sample4 groupA
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198 sample5 groupB
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199 sample6 groupB
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200 sample7 groupB
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201 sample8 groupB
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202 ======== =========
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203
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204 Note: No title/header in experiment design file and the first two lines of the experiment design must have keyword "case" and "control"
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205
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206 ]]>
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207 </help>
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208 <citations>
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209 <citation type="bibtex">
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210 @misc{QuanTP: A software resource for quantitative proteo-transcriptomic comparative data analysis and informatics,
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211 author={Praveen Kumar, Priyabrata Panigrahi, James Johnson, Wanda Weber, Subina Mehta, Ray Sajulga, Caleb Easterly, Brian Crooker, Mohammad Heydarian, Krishanpal Anamika, Timothy Griffin, and Pratik Jagtap},
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212 year={2018},
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213 title={QuanTP}
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214 }
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215 </citation>
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216 </citations>
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217 </tool>