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Uploaded new release 1.7.3
author lgueguen
date Thu, 07 Jan 2021 11:12:01 +0000
parents de6d0b7c17af
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3:de6d0b7c17af 4:05c9b1a7f44e
1 <macros> 1 <macros>
2 2
3 <token name="@WRAPPER_VERSION@">1.6.3</token> 3 <token name="@TOOL_VERSION@">1.7.3</token>
4 4
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="1.6.3">r-sartools</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">r-sartools</requirement>
8 <requirement type="package" version="1.6.0">r-optparse</requirement>
9 </requirements> 8 </requirements>
10 </xml> 9 </xml>
11 10
12 <xml name="stdio"> 11 <xml name="stdio">
13 <stdio> 12 <stdio>
21 level="fatal" 20 level="fatal"
22 description="rsync error" /> 21 description="rsync error" />
23 </stdio> 22 </stdio>
24 </xml> 23 </xml>
25 24
26 <token name="@COMMAND_BASIC_PARAMETERS@"> 25 <token name="@COMMAND_BASIC_PARAMETERS@">
27 --projectName $projectName 26 --projectName '$projectName'
28 --author $author 27 --author '$author'
29 --targetFile $targetFile 28 --targetFile '$targetFile'
30 --rawDir $rawDir 29 --rawDir '$rawDir'
31 --featuresToRemove $featuresToRemove 30 --featuresToRemove '$featuresToRemove'
32 --varInt $varInt 31 --varInt '$varInt'
33 --condRef $condRef 32 --condRef '$condRef'
34 </token> 33 </token>
35 34
36 <token name="@COMMAND_BATCH_PARAM@"> 35 <token name="@COMMAND_BATCH_PARAM@">
37 #if $advanced_parameters.batch_condition.condition: 36 #if $advanced_parameters.batch_condition.condition:
38 --batch $advanced_parameters.batch_condition.batch 37 --batch '$advanced_parameters.batch_condition.batch'
39 #else: 38 #else:
40 --batch NULL 39 --batch NULL
41 #end if 40 #end if
42 </token> 41 </token>
43 42
44 <token name="@COMMAND_OUTPUTS@"> 43 <token name="@COMMAND_OUTPUTS@">
45 --figures_html $figures_html 44 --figures_html '$figures_html'
46 --figures_html_files_path $figures_html.files_path 45 --figures_html_files_path '$figures_html.files_path'
47 --tables_html $tables_html 46 --tables_html '$tables_html'
48 --tables_html_files_path $tables_html.files_path 47 --tables_html_files_path '$tables_html.files_path'
49 --rdata $rdata 48 --rdata '$rdata'
50 --report_html $report_html 49 --report_html '$report_html'
51 --log $log 50 --log '$log'
52 </token> 51 </token>
53 52
54 <macro name="basic_parameters"> 53 <macro name="basic_parameters">
55 <param type="text" value="Project" label="Name of the project used for the report" argument="--projectName" help="No space allowed." > 54 <param type="text" value="Project" label="Name of the project used for the report" argument="--projectName" help="No space allowed." >
56 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator> 55 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator>
57 </param> 56 </param>
58 <param type="text" value="Galaxy" label="Name of the report author" argument="--author" help="No space allowed." > 57 <param type="text" value="Galaxy" label="Name of the report author" argument="--author" help="No space allowed." >
59 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator> 58 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator>
60 </param> 59 </param>
61 <param type="data" format="txt" label="Design / target file" argument="--targetFile" help="See the help section below for details on the required format." /> 60 <param type="data" format="txt" label="Design / target file" argument="--targetFile" help="See the help section below for details on the required format." />
62 <param type="data" format="no_unzip.zip,zip" label="Zip file containing raw counts files" argument="--rawDir" help="See the help section below for details on the required format." /> 61 <param type="data" format="no_unzip.zip,zip" label="Zip file containing raw counts files" argument="--rawDir" help="See the help section below for details on the required format." />
63 <param type="text" size="100" value="alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual" label="Names of the features to be removed" argument="--featuresToRemove" help="Separate the features with a comma, no space allowed. More than once can be specified. Specific HTSeq-count information and rRNA for example. Default are 'alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual'." > 62 <param type="text" size="100" value="alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual" label="Names of the features to be removed" argument="--featuresToRemove" help="Separate the features with a comma, no space allowed. More than once can be specified. Specific HTSeq-count information and rRNA for example. Default are 'alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual'." >
64 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator> 63 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator>
65 </param> 64 </param>
66 <param type="text" value="group" label="Factor of interest" argument="--varInt" help="Biological condition in the target file. Default is 'group'." > 65 <param type="text" value="group" label="Factor of interest" argument="--varInt" help="Biological condition in the target file. Default is 'group'." >
67 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator> 66 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator>
68 </param> 67 </param>
69 <param type="text" value="WT" label="Reference biological condition" argument="--condRef" help="Reference biological condition used to compute fold-changes, must be one of the levels of 'Factor of interest'." > 68 <param type="text" value="WT" label="Reference biological condition" argument="--condRef" help="Reference biological condition used to compute fold-changes, must be one of the levels of 'Factor of interest'." >
70 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator> 69 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator>
71 </param> 70 </param>
72 </macro> 71 </macro>
73 72
74 <macro name="batch_param"> 73 <macro name="batch_param">
75 <conditional name="batch_condition"> 74 <conditional name="batch_condition">
76 <param name="condition" type="boolean" checked="false" truevalue="batch" falsevalue="NULL" label="Add a blocking factor" argument="--batch" help="Adjustment variable to use as a batch effect. Default: unchecked if no batch effect needs to be taken into account."/> 75 <param name="condition" type="boolean" checked="false" truevalue="batch" falsevalue="NULL" label="Add a blocking factor" argument="--batch" help="Adjustment variable to use as a batch effect. Default: unchecked if no batch effect needs to be taken into account."/>
77 <when value="NULL" /> 76 <when value="NULL" />
78 <when value="batch"> 77 <when value="batch">
79 <param name="batch" type="text" value="batch" label="Blocking factor value" help="Must be a column of the target file" > 78 <param name="batch" type="text" value="batch" label="Blocking factor value" help="Must be a column of the target file" >
80 <validator type="empty_field"/> 79 <validator type="empty_field"/>
81 </param> 80 </param>
82 </when> 81 </when>
83 </conditional> 82 </conditional>
84 </macro> 83 </macro>
85 84
86 <macro name="alpha_param"> 85 <macro name="alpha_param">
87 <param type="float" value="0.05" min="0" max="1" label="Threshold of statistical significance" argument="--alpha" help="Significance threshold applied to the adjusted p-values to select the differentially expressed features. Default is 0.05. The comma is not allowed as decimal separator, use a point instead." /> 86 <param type="float" value="0.05" min="0" max="1" label="Threshold of statistical significance" argument="--alpha" help="Significance threshold applied to the adjusted p-values to select the differentially expressed features. Default is 0.05. The comma is not allowed as decimal separator, use a point instead." />
88 </macro> 87 </macro>
89 88
90 <macro name="padjustmethod_param"> 89 <macro name="padjustmethod_param">
91 <param type="select" label="p-value adjustment method" argument="--pAdjustMethod" help="p-value adjustment method for multiple testing. 'BH' by default, 'BY' or any value of p.adjust.methods." > 90 <param type="select" label="p-value adjustment method" argument="--pAdjustMethod" help="p-value adjustment method for multiple testing. 'BH' by default, 'BY' or any value of p.adjust.methods." >
92 <option value="BH" selected="true">BH</option> 91 <option value="BH" selected="true">BH</option>
93 <option value="BY">BY</option> 92 <option value="BY">BY</option>
94 <option value="bonferroni">bonferroni</option> 93 <option value="bonferroni">bonferroni</option>
95 <option value="fdr">fdr</option> 94 <option value="fdr">fdr</option>
96 <option value="hochberg">hochberg</option> 95 <option value="hochberg">hochberg</option>
97 <option value="holm">holm</option> 96 <option value="holm">holm</option>
98 <option value="hommel">hommel</option> 97 <option value="hommel">hommel</option>
99 </param> 98 </param>
100 </macro> 99 </macro>
101 100
102 <macro name="colors_param"> 101 <macro name="colors_param">
103 <param type="text" size="100" value="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange" label="Colors of each biological condition on the plots: 'col1,col2,col3,col4'" argument="--colors" help="Separate the colors with a comma, no space allowed. Default are 'dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange'." > 102 <param type="text" size="100" value="#f3c300,#875692,#f38400,#a1caf1,#be0032,#c2b280,#848482,#008856,#e68fac,#0067a5" label="Colors of each biological condition on the plots: 'col1,col2,col3,col4'" argument="--colors" help="Separate the colors with a comma, no space allowed. Default are '#f3c300,#875692,#f38400,#a1caf1,#be0032,#c2b280,#848482,#008856,#e68fac,#0067a5'." >
104 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator> 103 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator>
105 </param> 104 <sanitizer>
106 </macro> 105 <valid>
107 106 <add value="#" />
108 <macro name="forceCairoGraph_param"> 107 </valid>
109 <param type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Activate cairo type" argument="--forceCairoGraph" help="Unchecked by default." /> 108 </sanitizer>
110 </macro> 109 </param>
111 110 </macro>
112 <macro name="outputs"> 111
112 <macro name="forceCairoGraph_param">
113 <param type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Activate cairo type" argument="--forceCairoGraph" help="Unchecked by default." />
114 </macro>
115
116 <macro name="outputs">
113 <data name="report_html" format="html" label="${tool.name} report" /> 117 <data name="report_html" format="html" label="${tool.name} report" />
114 <data name="tables_html" format="html" label="${tool.name} tables" /> 118 <data name="tables_html" format="html" label="${tool.name} tables" />
115 <data name="figures_html" format="html" label="${tool.name} figures" /> 119 <data name="figures_html" format="html" label="${tool.name} figures" />
116 <data name="log" format="txt" label="${tool.name} R log" /> 120 <data name="log" format="txt" label="${tool.name} R log" />
117 <data name="rdata" format="data" label="${tool.name} R objects (.RData)" /> 121 <data name="rdata" format="data" label="${tool.name} R objects (.RData)" />
118 </macro> 122 </macro>
119 123
120 <token name="@HELP_AUTHORS@"> 124 <token name="@HELP_AUTHORS@">
121 .. class:: infomark 125 .. class:: infomark
122 126
123 **Authors** M.-A. Dillies and H. Varet 127 **Authors** M.-A. Dillies and H. Varet
124 128
125 | If you use this tool, please cite: H. Varet, L. Brillet-Guéguen, J.-Y. Coppee and M.-A. Dillies, SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data, PLoS One, 2016, doi: http://dx.doi.org/10.1371/journal.pone.0157022 129 | If you use this tool, please cite: H. Varet, L. Brillet-Guéguen, J.-Y. Coppee and M.-A. Dillies, SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data, PLoS One, 2016, doi: http://dx.doi.org/10.1371/journal.pone.0157022
130 **Galaxy integration** Loraine Brillet-Guéguen, Institut Français de Bioinformatique 134 **Galaxy integration** Loraine Brillet-Guéguen, Institut Français de Bioinformatique
131 135
132 | Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool. 136 | Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.
133 137
134 --------------------------------------------------- 138 ---------------------------------------------------
135 </token> 139 </token>
136 140
137 <token name="@HELP_DESCRIPTION@"> 141 <token name="@HELP_DESCRIPTION@">
138 | SARTools is a R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 or edgeR packages and to export the results into easily readable tab-delimited files. It also facilitates the generation of a HTML report which displays all the figures produced, explains the statistical methods and gives the results of the differential analysis. 142 | SARTools is a R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 or edgeR packages and to export the results into easily readable tab-delimited files. It also facilitates the generation of a HTML report which displays all the figures produced, explains the statistical methods and gives the results of the differential analysis.
139 | Note that SARTools does not intend to replace DESeq2 or edgeR: it simply provides an environment to go with them. For more details about the methodology behind DESeq2 or edgeR, the user should read their documentations and papers. 143 | Note that SARTools does not intend to replace DESeq2 or edgeR: it simply provides an environment to go with them. For more details about the methodology behind DESeq2 or edgeR, the user should read their documentations and papers.
140 </token> 144 </token>
141 145
142 <token name="@HELP_INPUT_FILES@"> 146 <token name="@HELP_INPUT_FILES@">
143 .. class:: warningmark 147 .. class:: warningmark
144 148
145 If the counts and the target files are not supplied in the required formats, the workflow will probably crash and will not be able to run the analysis. 149 If the counts and the target files are not supplied in the required formats, the workflow will probably crash and will not be able to run the analysis.
146 150
147 151
153 | 2 : Raw counts files | zip | 157 | 2 : Raw counts files | zip |
154 +---------------------------+-----------+ 158 +---------------------------+-----------+
155 159
156 160
157 Design/target file: 161 Design/target file:
158 | The user has to supply a tab delimited file which describes the experiment, i.e. which contains the name of the biological condition associated with each sample. This file is called ”target” as a reference to the target file needed when using the limma package [1]. This file has one row per sample and is composed of at least three columns with headers: 162 | The user has to supply a tab delimited file which describes the experiment, i.e. which contains the name of the biological condition associated with each sample. This file is called ”target” as a reference to the target file needed when using the limma package [1]. This file has one row per sample and is composed of at least three columns with headers:
159 163
160 * column 1 : unique names of the samples (short but informative as they will be displayed on all the figures); 164 * column 1 : unique names of the samples (short but informative as they will be displayed on all the figures);
161 * column 2 : name of the count files; 165 * column 2 : name of the count files;
162 * column 3 : biological conditions; 166 * column 3 : biological conditions;
163 * optional columns : further information about the samples (day of library preparation for example). 167 * optional columns : further information about the samples (day of library preparation for example).
164 168
165 169
166 - Example of a target file:: 170 - Example of a target file::
167 171
168 label files group 172 label files group
171 s1c2 count_file_sample1_cond2.txt cond2 175 s1c2 count_file_sample1_cond2.txt cond2
172 s2c2 count_file_sample2_cond2.txt cond2 176 s2c2 count_file_sample2_cond2.txt cond2
173 177
174 178
175 Zip file containing raw counts files: 179 Zip file containing raw counts files:
176 | The statistical analysis assumes that reads have already been mapped and that counts per feature (gene or transcript) are available. If counting has been done with HTSeq-count [2, 3], output files are ready to be loaded in R with the dedicated SARTools function. If not, the user must supply, in a zip file, one count file per sample with two tab delimited columns without header: 180 | The statistical analysis assumes that reads have already been mapped and that counts per feature (gene or transcript) are available. If counting has been done with HTSeq-count [2, 3], output files are ready to be loaded in R with the dedicated SARTools function. If not, the user must supply, in a zip file, one count file per sample with two tab delimited columns without header:
177 181
178 * column 1 : the unique IDs of the features; 182 * column 1 : the unique IDs of the features;
179 * column 2 : the raw counts associated with these features (null or positive integers). 183 * column 2 : the raw counts associated with these features (null or positive integers).
180 </token> 184 </token>
181 185
182 <token name="@HELP_BASIC_PARAMETERS@"> 186 <token name="@HELP_BASIC_PARAMETERS@">
183 * **projectName:** name of the project; 187 * **projectName:** name of the project;
184 * **author:** author of the analysis; 188 * **author:** author of the analysis;
185 * **featuresToRemove:** character vector containing the IDs of the features to remove before running the analysis (default are "alignment not unique", "ambiguous", "no feature", "not aligned", "too low aQual" to remove HTSeq-count specific rows); 189 * **featuresToRemove:** character vector containing the IDs of the features to remove before running the analysis (default are "alignment not unique", "ambiguous", "no feature", "not aligned", "too low aQual" to remove HTSeq-count specific rows);
186 * **varInt:** variable of interest, i.e. biological condition, in the target file ("group" by default); 190 * **varInt:** variable of interest, i.e. biological condition, in the target file ("group" by default);
187 * **condRef:** reference biological condition used to compute fold-changes (no default, must be one of the levels of varInt); 191 * **condRef:** reference biological condition used to compute fold-changes (no default, must be one of the levels of varInt);
188 </token> 192 </token>
189 193
190 <token name="@HELP_OUTPUT_FILES@"> 194 <token name="@HELP_OUTPUT_FILES@">
191 **Report:** 195 **Report:**
192 196
193 197
194 | Give details about the methodology, the different steps and the results. It displays all the figures produced and the most important results of the differential analysis as the number of up- and down-regulated features. 198 | Give details about the methodology, the different steps and the results. It displays all the figures produced and the most important results of the differential analysis as the number of up- and down-regulated features.
195 | The user should read the full HTML report and closely analyze each figure to check that the analysis ran smoothly. 199 | The user should read the full HTML report and closely analyze each figure to check that the analysis ran smoothly.
196 200
197 201
198 **Tables:** 202 **Tables:**
199 203
200 204
201 * **TestVsRef.complete.txt:** contains all the features studied; 205 * **TestVsRef.complete.txt:** contains all the features studied;
202 * **TestVsRef.down.txt:** contains only significant down-regulated features, i.e. less expressed in Test than in Ref; 206 * **TestVsRef.down.txt:** contains only significant down-regulated features, i.e. less expressed in Test than in Ref;
203 * **TestVsRef.up.txt:** contains only significant up-regulated features i.e. more expressed in Test than in Ref. 207 * **TestVsRef.up.txt:** contains only significant up-regulated features i.e. more expressed in Test than in Ref.
204 208
205 209
206 **Figures:** 210 **Figures:**
207 211
208 212
209 * **MAplot.png:** MA-plot for each comparison (log ratio of the means vs intensity). 213 * **MAplot.png:** MA-plot for each comparison (log ratio of the means vs intensity).
210 * **PCA.png:** first and second factorial planes of the PCA on the samples based on VST or rlog data; 214 * **PCA.png:** first and second factorial planes of the PCA on the samples based on VST or rlog data;
211 * **barplotNull.png:** percentage of null counts per sample; 215 * **barplotNull.png:** percentage of null counts per sample;
212 * **barplotTC.png:** total number of reads per sample; 216 * **barplotTC.png:** total number of reads per sample;
213 * **cluster.png:** hierachical clustering of the samples (based on VST or rlog data); 217 * **cluster.png:** hierachical clustering of the samples (based on VST or rlog data);
214 * **countsBoxplot.png:** boxplots on raw and normalized counts; 218 * **countsBoxplot.png:** boxplots on raw and normalized counts;
215 * **densplot.png:** estimation of the density of the counts for each sample; 219 * **densplot.png:** estimation of the density of the counts for each sample;
216 * **diagSizeFactorsHist.png:** diagnostic of the estimation of the size factors; 220 * **diagSizeFactorsHist.png:** diagnostic of the estimation of the size factors;
217 * **diagSizeFactorsTC.png:** plot of the size factors vs the total number of reads; 221 * **diagSizeFactorsTC.png:** plot of the size factors vs the total number of reads;
218 * **dispersionsPlot.png:** graph of the estimations of the dispersions and diagnostic of log-linearity of the dispersions; 222 * **dispersionsPlot.png:** graph of the estimations of the dispersions and diagnostic of log-linearity of the dispersions;
219 * **majSeq.png:** percentage of reads caught by the feature having the highest count in each sample; 223 * **majSeq.png:** percentage of reads caught by the feature having the highest count in each sample;
220 * **pairwiseScatter.png:** pairwise scatter plot between each pair of samples and SERE values; 224 * **pairwiseScatter.png:** pairwise scatter plot between each pair of samples and SERE values;
221 * **rawpHist.png:** histogram of the raw p-values for each comparison; 225 * **rawpHist.png:** histogram of the raw p-values for each comparison;
222 * **volcanoPlot.png:** vulcano plot for each comparison (− log10 (adjusted P value) vs log ratio of the means). 226 * **volcanoPlot.png:** vulcano plot for each comparison (− log10 (adjusted P value) vs log ratio of the means).
223 227
224 228
225 **R log file:** 229 **R log file:**
226 230
227 231
228 | Give the R console outputs. 232 | Give the R console outputs.
229 233
230 234
231 **R objects (.RData file):** 235 **R objects (.RData file):**
232 236
233 237
234 | Give all the R objects created during the analysis is saved: it may be used to perform downstream analyses. 238 | Give all the R objects created during the analysis is saved: it may be used to perform downstream analyses.
235 </token> 239 </token>
236 240
237 <macro name="common_citations"> 241 <macro name="common_citations">
238 <citation type="doi">10.1371/journal.pone.0157022</citation> 242 <citation type="doi">10.1371/journal.pone.0157022</citation>
239 <citation type="bibtex">@INBOOK{Smyth05, 243 <citation type="bibtex">@INBOOK{Smyth05,
240 author = {G.-K. Smyth}, 244 author = {G.-K. Smyth},
241 editor = {R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, and W. Huber}, 245 editor = {R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, and W. Huber},
242 chapter = {Limma: linear models for microarray data}, 246 chapter = {Limma: linear models for microarray data},
243 title = {Bioinformatics and Computational Biology Solutions Using R and Bioconductor}, 247 title = {Bioinformatics and Computational Biology Solutions Using R and Bioconductor},
244 publisher = {Springer}, 248 publisher = {Springer},
245 year = {2005}, 249 year = {2005},
246 pages = {397–420} 250 pages = {397–420}
247 }</citation> 251 }</citation>
248 <citation type="doi">10.1093/bioinformatics/btu638</citation> 252 <citation type="doi">10.1093/bioinformatics/btu638</citation>
249 <citation type="bibtex">@ARTICLE{Benjamini95, 253 <citation type="bibtex">@ARTICLE{Benjamini95,
250 author = {Y. Benjamini and Y. Hochberg}, 254 author = {Y. Benjamini and Y. Hochberg},
251 title = {Controlling the false discovery rate: a practical and powerful approach to multiple testing}, 255 title = {Controlling the false discovery rate: a practical and powerful approach to multiple testing},
252 journal = {Journal of the Royal Statistical Society B}, 256 journal = {Journal of the Royal Statistical Society B},
253 year = {1995}, 257 year = {1995},
254 volume = {57}, 258 volume = {57},
255 pages = {289–300} 259 pages = {289–300}
256 }</citation> 260 }</citation>
257 <citation type="bibtex">@ARTICLE{Benjamini01, 261 <citation type="bibtex">@ARTICLE{Benjamini01,
258 author = {Y. Benjamini and D. Yekutieli}, 262 author = {Y. Benjamini and D. Yekutieli},
259 title = {The control of the false discovery rate in multiple testing under dependency}, 263 title = {The control of the false discovery rate in multiple testing under dependency},
260 journal = {Ann. Statist.}, 264 journal = {Ann. Statist.},
261 year = {2001}, 265 year = {2001},
262 volume = {29}, 266 volume = {29},
263 number = {4}, 267 number = {4},
264 pages = {1165–1188} 268 pages = {1165–1188}
265 }</citation> 269 }</citation>
266 </macro> 270 </macro>
267 271
268 </macros> 272 </macros>