Mercurial > repos > shians > shrnaseq
annotate hairpinTool.xml @ 13:7aaa9bc23e3c
Added support for paired end reads
- Changed terminology to generalise to sgRNA CRISPR experiments.
- Added option to include second factor for statistical power
- Added option to filter out samples with low counts
- Added support for paired end reads
- Added option to highlight only positive or negative fold change in smear plot
- Fixed bug that caused tool to stop if more than enough sample annotations
were supplied
| author | shian_su <registertonysu@gmail.com> |
|---|---|
| date | Tue, 14 Oct 2014 17:05:07 +1100 |
| parents | c0a76e30d61b |
| children | 44130e484a97 |
| rev | line source |
|---|---|
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1 <tool id="shRNAseq" name="shRNAseq Tool" version="1.2.0"> |
| 2 | 2 <description> |
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3 Analyse differential representation for shRNAseq and sgRNA based procedures |
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4 using edgeR package from Bioconductor. |
| 2 | 5 </description> |
| 6 | |
| 7 <requirements> | |
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8 <requirement type="R-module" version="3.7.17">edgeR</requirement> |
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9 <requirement type="R-module" version="3.21.16">limma</requirement> |
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10 <requirement type="package" version="3.1.1">R_3_0_3</requirement> |
| 2 | 11 </requirements> |
| 12 | |
| 13 <stdio> | |
| 14 <exit_code range="1:" level="fatal" description="Tool exception" /> | |
| 15 </stdio> | |
| 16 | |
| 17 <command interpreter="Rscript"> | |
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18 ampliconTool.R $inputOpt.inputType |
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19 #if $inputOpt.inputType=="fastq": |
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20 |
| 2 | 21 #for $i, $fas in enumerate($inputOpt.fastq): |
| 22 fastq::$fas.file | |
| 23 #end for | |
| 24 | |
| 25 $inputOpt.hairpin | |
| 26 $inputOpt.samples | |
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27 |
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28 #if $inputOpt.positions.posOption=="yes": |
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29 $inputOpt.positions.barstart |
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30 $inputOpt.positions.barend |
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31 0 |
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32 0 |
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33 $inputOpt.positions.hpstart |
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34 $inputOpt.positions.hpend |
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35 #else: |
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36 1 |
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37 5 |
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38 0 |
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39 0 |
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40 37 |
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41 57 |
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42 #end if |
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43 #elif $inputOpt.inputType=="pairedFastq": |
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44 |
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45 #for $i, $fas in enumerate($inputOpt.fastq): |
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46 fastq::$fas.file |
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47 #end for |
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48 |
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49 #for $i, $fas in enumerate($inputOpt.fastq): |
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50 fastqRev::$fas.fileRev |
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51 #end for |
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52 |
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53 $inputOpt.hairpin |
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54 $inputOpt.samples |
| 2 | 55 |
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56 #if $inputOpt.positions.posOption=="yes": |
| 2 | 57 $inputOpt.positions.barstart |
| 58 $inputOpt.positions.barend | |
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59 $inputOpt.positions.barstartRev |
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60 $inputOpt.positions.barendRev |
| 2 | 61 $inputOpt.positions.hpstart |
| 62 $inputOpt.positions.hpend | |
| 63 #else: | |
| 64 1 | |
| 65 5 | |
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66 0 |
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67 0 |
| 2 | 68 37 |
| 69 57 | |
| 70 #end if | |
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71 |
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72 #elif $inputOpt.inputType=="counts": |
| 2 | 73 $inputOpt.counts |
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74 $inputOpt.hairpin |
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75 $inputOpt.samples |
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76 0 |
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77 0 |
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78 0 |
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79 0 |
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80 0 |
| 2 | 81 #end if |
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82 |
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83 #if $inputOpt.secondaryFactor.secFactorOpt=="yes": |
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84 $inputOpt.secondaryFactor.secFactName |
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85 #else: |
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86 "none" |
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87 #end if |
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88 |
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89 #if $filterCPM.filtOption=="yes": |
| 2 | 90 $filterCPM.cpmReq |
| 91 $filterCPM.sampleReq | |
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92 $filterCPM.readReq |
| 2 | 93 #else: |
| 94 -Inf | |
| 95 -Inf | |
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96 -Inf |
| 2 | 97 #end if |
| 98 | |
| 99 $fdr | |
| 100 $lfc | |
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101 $direction |
| 2 | 102 $workMode.mode |
| 103 $outFile | |
| 104 $outFile.files_path | |
| 105 | |
| 106 #if $workMode.mode=="classic": | |
| 107 "$workMode.pair1" | |
| 108 "$workMode.pair2" | |
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109 #elif $workMode.mode=="glm": |
| 2 | 110 "$workMode.contrast" |
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111 $workMode.roast.roastOption |
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112 |
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113 #if $workMode.roast.roastOption=="yes": |
| 2 | 114 $workMode.roast.hairpinReq |
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115 $workMode.roast.select.selOption |
| 2 | 116 "$workMode.roast.select.selection" |
| 117 #else: | |
| 118 0 | |
| 119 0 | |
| 120 0 | |
| 121 #end if | |
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122 |
| 2 | 123 #end if |
| 124 </command> | |
| 125 | |
| 126 <inputs> | |
| 127 <conditional name="inputOpt"> | |
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128 |
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129 <param name="inputType" type="select" label="Input File Type"> |
| 2 | 130 <option value="fastq">FastQ File</option> |
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131 <option value="pairedFastq">Paired FastQ File</option> |
| 2 | 132 <option value="counts">Table of Counts</option> |
| 133 </param> | |
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134 |
| 2 | 135 <when value="fastq"> |
| 136 <param name="hairpin" type="data" format="tabular" | |
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137 label="Target Annotation"/> |
| 2 | 138 |
| 139 <param name="samples" type="data" format="tabular" | |
| 140 label="Sample Annotation"/> | |
| 141 | |
| 142 <repeat name="fastq" title="FastQ Files"> | |
| 143 <param name="file" type="data" format="fastq"/> | |
| 144 </repeat> | |
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145 |
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146 <conditional name="secondaryFactor"> |
| 2 | 147 |
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148 <param name="secFactorOpt" type="select" |
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149 label="Include Secondary Factor"> |
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150 |
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151 <option value="no" selected="True">No</option> |
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152 |
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153 <option value="yes">Yes</option> |
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154 |
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155 </param> |
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156 |
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157 <when value="yes"> |
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158 |
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159 <param name="secFactName" type="text" label="Secondary Factor Name" |
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160 size="80"/> |
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161 |
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162 </when> |
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163 |
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164 <when value="no"> |
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165 </when> |
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166 </conditional> |
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167 |
| 2 | 168 <conditional name="positions"> |
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169 <param name="posOption" type="select" |
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170 label="Specify Sample Index and Target Sequence Locations?" |
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171 help="Default Positions: Index: 1 to 5, Target: 37 to 57."> |
| 2 | 172 <option value="no" selected="True">No</option> |
| 173 <option value="yes">Yes</option> | |
| 174 </param> | |
| 175 | |
| 176 <when value="yes"> | |
| 177 <param name="barstart" type="integer" value="1" | |
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178 label="Index Starting Position"/> |
| 2 | 179 <param name="barend" type="integer" value="5" |
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180 label="Index Ending Position"/> |
| 2 | 181 |
| 182 <param name="hpstart" type="integer" value="37" | |
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183 label="Target Starting Position"/> |
| 2 | 184 |
| 185 <param name="hpend" type="integer" value="57" | |
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186 label="Target Ending Position"/> |
| 2 | 187 </when> |
| 188 | |
| 189 <when value="no"/> | |
| 190 </conditional> | |
| 191 </when> | |
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192 |
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193 <when value="pairedFastq"> |
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194 <param name="hairpin" type="data" format="tabular" |
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195 label="Target Sequence Annotation"/> |
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196 |
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197 <param name="samples" type="data" format="tabular" |
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198 label="Sample Annotation"/> |
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199 |
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200 <repeat name="fastq" title="FastQ Files"> |
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201 <param name="file" type="data" format="fastq"/> |
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202 <param name="fileRev" type="data" format="fastq"/> |
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203 </repeat> |
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204 |
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205 <conditional name="secondaryFactor"> |
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206 |
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207 <param name="secFactorOpt" type="select" |
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208 label="Include Secondary Factor"> |
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209 |
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210 <option value="no" selected="True">No</option> |
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211 |
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212 <option value="yes">Yes</option> |
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213 |
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214 </param> |
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215 |
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216 <when value="yes"> |
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217 |
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218 <param name="secFactName" type="text" label="Secondary Factor Name" |
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219 size="80"/> |
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220 |
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221 </when> |
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222 |
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223 <when value="no"> |
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224 </when> |
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225 </conditional> |
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226 |
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227 <conditional name="positions"> |
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228 |
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229 <param name="posOption" type="select" |
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230 label="Specify Sample Index and Target Sequence Locations?" |
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231 help="Default Positions: Index: 1 to 5, Input required for |
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232 reverse end, Target: 37 to 57."> |
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233 |
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234 <option value="no" selected="True">No</option> |
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235 |
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236 <option value="yes">Yes</option> |
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237 |
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238 </param> |
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239 |
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240 <when value="yes"> |
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241 <param name="barstart" type="integer" value="1" |
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242 label="Index Starting Position"/> |
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243 |
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244 <param name="barend" type="integer" value="5" |
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245 label="Index Ending Position"/> |
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246 |
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247 <param name="barstartRev" type="integer" value="0" |
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248 label="Reverse Index Starting Position"/> |
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249 |
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250 <param name="barendRev" type="integer" value="0" |
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251 label="Reverse Index Ending Position"/> |
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252 |
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253 <param name="hpstart" type="integer" value="37" |
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254 label="Target Starting Position"/> |
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255 |
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256 <param name="hpend" type="integer" value="57" |
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257 label="Target Ending Position"/> |
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258 </when> |
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259 |
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260 <when value="no"> |
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261 </when> |
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262 |
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263 </conditional> |
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264 |
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265 </when> |
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266 |
| 2 | 267 <when value="counts"> |
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268 |
| 2 | 269 <param name="counts" type="data" format="tabular" label="Counts Table"/> |
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270 |
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271 <param name="hairpin" type="data" format="tabular" |
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272 label="Target Sequence Annotation"/> |
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273 |
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274 <param name="samples" type="data" format="tabular" |
| 2 | 275 label="Sample Annotation"/> |
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276 |
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277 <conditional name="secondaryFactor"> |
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278 |
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279 <param name="secFactorOpt" type="select" |
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280 label="Include Secondary Factor"> |
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281 |
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282 <option value="no" selected="True">No</option> |
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283 |
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284 <option value="yes">Yes</option> |
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285 |
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286 </param> |
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287 |
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288 <when value="yes"> |
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289 |
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290 <param name="secFactName" type="text" label="Secondary Factor Name" |
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291 size="80"/> |
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292 |
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293 </when> |
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294 |
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295 <when value="no"> |
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296 </when> |
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297 |
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298 </conditional> |
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299 |
| 2 | 300 </when> |
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301 |
| 2 | 302 </conditional> |
| 303 | |
| 304 <conditional name="filterCPM"> | |
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305 <param name="filtOption" type="select" label="Filter Low CPM?" |
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306 help="Ignore target sequences with very low representation when |
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307 performing analysis."> |
| 2 | 308 <option value="yes">Yes</option> |
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309 <option value="no">No</option> |
| 2 | 310 </param> |
| 311 | |
| 312 <when value="yes"> | |
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313 <param name="cpmReq" type="float" value="0.5" min="0" |
| 2 | 314 label="Minimum CPM"/> |
| 315 | |
| 316 <param name="sampleReq" type="integer" value="1" min="0" | |
| 317 label="Minimum Samples" | |
| 318 help="Filter out all the genes that do not meet the minimum | |
| 319 CPM in at least this many samples."/> | |
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320 |
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321 <param name="readReq" type="integer" value="1000" min="0" |
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322 label="Minimum Reads" |
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323 help="Filter out all samples that do not have the minimum |
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324 number of reads."/> |
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325 |
| 2 | 326 </when> |
| 327 | |
| 328 <when value="no"/> | |
| 329 | |
| 330 </conditional> | |
| 331 | |
| 332 <conditional name="workMode"> | |
| 333 <param name="mode" type="select" label="Analysis Type" | |
| 334 help="Classic Exact Tests are useful for simple comparisons across | |
| 335 two sampling groups. Generalised linear models allow for more | |
| 336 complex contrasts and gene level analysis to be made."> | |
| 337 <option value="classic">Classic Exact Test</option> | |
| 338 <option value="glm">Generalised Linear Model</option> | |
| 339 </param> | |
| 340 | |
| 341 <when value="classic"> | |
| 342 <param name="pair1" type="text" label="Compare" size="40"/> | |
| 343 <param name="pair2" type="text" label="To" size="40" | |
| 344 help="The analysis will subtract values of this group from those | |
| 345 in the group above to establish the difference."/> | |
| 346 </when> | |
| 347 | |
| 348 <when value="glm"> | |
| 349 <param name="contrast" type="text" size="60" | |
| 350 label="Contrasts of interest" | |
| 351 help="Specify equations defining contrasts to be made. Eg. | |
| 352 KD-Control will result in positive fold change if KD has | |
| 353 greater expression and negative if Control has greater | |
| 354 expression."/> | |
| 355 | |
| 356 <conditional name="roast"> | |
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357 <param name="roastOption" type="select" |
| 2 | 358 label="Perform Gene Level Analysis?" |
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359 help="Analyse LogFC tendencies for target sequences belonging |
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360 to the same gene. NOTE: this is a slow procedure that |
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361 scales badly with the number of genes analysed."> |
| 2 | 362 <option value="no">No</option> |
| 363 <option value="yes">Yes</option> | |
| 364 </param> | |
| 365 | |
| 366 <when value="yes"> | |
| 367 <param name="hairpinReq" type="integer" value="2" min="2" | |
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368 label="Minimum Targets Found" |
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369 help="Only genes with at least this many target sequences |
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370 found will be analysed."/> |
| 2 | 371 |
| 372 <conditional name="select"> | |
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373 <param name="selOption" type="select" |
| 2 | 374 label="Gene Selection Method"> |
| 375 <option value="rank">By p-value Rank</option> | |
| 376 <option value="geneID">By Gene Identifier</option> | |
| 377 </param> | |
| 378 <when value="rank"> | |
| 379 <param name="selection" type="text" size="40" value="1:5" | |
| 380 label="Ranks of Top Genes to Plot" | |
| 381 help="Genes are ranked in ascending p-value for | |
| 382 differential representation, individual ranks can | |
| 383 be entered seperated by comma or a range seperated | |
| 384 by colon."/> | |
| 385 </when> | |
| 386 <when value="geneID"> | |
| 387 <param name="selection" type="text" size="80" value="" | |
| 388 label="Symbols of Genes to Plot" | |
| 389 help="Select genes based on their identifier in the | |
| 390 'Gene' column of the sample information file. | |
| 391 Please ensure exact match with the values in input | |
| 392 file and separate selections with commas."/> | |
| 393 </when> | |
| 394 </conditional> | |
| 395 | |
| 396 | |
| 397 </when> | |
| 398 | |
| 399 <when value="no"/> | |
| 400 </conditional> | |
| 401 </when> | |
| 402 </conditional> | |
| 403 | |
| 404 <param name="fdr" type="float" value="0.05" min="0" max="1" | |
| 405 label="FDR Threshold" | |
| 406 help="All observations below this threshold will be highlighted | |
| 407 in the smear plot."/> | |
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408 |
| 2 | 409 <param name="lfc" type="float" value="0" min="0" |
| 410 label="Absolute LogFC Threshold" | |
| 411 help="In additional to meeting the FDR requirement, the absolute | |
| 412 value of the log-fold-change of the observation must be above | |
| 413 this threshold to be highlighted."/> | |
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414 |
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415 <param name="direction" type="select" label="Highlight Option" |
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416 help="Only hightlight positive or negative fold changes in smear plot?"> |
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417 <option value="all">Default</option> |
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418 <option value="up">Positive Only</option> |
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419 <option value="down">Negative Only</option> |
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420 </param> |
| 2 | 421 </inputs> |
| 422 | |
| 423 <outputs> | |
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424 <data format="html" name="outFile" label="TagSeq Analysis"/> |
| 2 | 425 </outputs> |
| 426 <help> | |
| 427 .. class:: infomark | |
| 428 | |
| 429 **What it does** | |
| 430 | |
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431 Given tables containing information about the hairpins/sgRNA and their |
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432 associated sample indices, information about the samples and fastq file |
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433 containing the sequencing reads. This tool will generate plots and tables for |
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434 the analysis of differential representation. |
| 2 | 435 |
| 7 | 436 .. class:: infomark |
| 437 | |
| 438 A tutorial of how to use this tool is available at: | |
| 439 http://bioinf.wehi.edu.au/shRNAseq/galaxy.html | |
| 440 | |
| 2 | 441 ----- |
| 442 | |
| 443 .. class:: infomark | |
| 444 | |
| 445 **INPUTS** | |
| 446 | |
| 447 **Input File Type:** | |
| 448 | |
| 449 This tool is able to either generate counts from a raw FastQ file given the | |
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450 information regarding the samples and hairpins/sgRNA. Alternatively if a table |
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451 of counts has already been generated it can also be used. |
| 2 | 452 |
| 453 **Counts Table (Counts Input):** | |
| 454 | |
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455 A tab delimited text table of information regarding the counts of |
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456 hairpins/sgRNA. Should have a column 'ID' to denote the hairpins/sgRNA that |
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457 counts correspond to. Each additional column should have titles corresponding to |
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458 the label for the sample. |
| 2 | 459 |
| 460 Example:: | |
| 461 | |
| 462 ID Sample1 Sample2 Sample3 | |
| 463 Control1 49802 48014 40148 | |
| 464 Control2 12441 16352 14232 | |
| 465 Control3 9842 9148 9111 | |
| 466 Hairpin1 3300 3418 2914 | |
| 467 Hairpin2 91418 95812 93174 | |
| 468 Hairpin3 32985 31975 35104 | |
| 469 Hairpin4 12082 14081 14981 | |
| 470 Hairpin5 2491 2769 2691 | |
| 471 Hairpin6 1294 1486 1642 | |
| 472 Hairpin7 49501 49076 47611 | |
| 473 ... | |
| 474 | |
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475 **Target Sequence Annotation:** |
| 2 | 476 |
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477 A tab delimited text table of information regarding the targetted |
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478 hairpins/sgRNA sequence. Should have columns 'ID', 'Sequences' and 'Gene' to |
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479 uniquely identify the target, align it with the reads to produce counts and |
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480 identify which gene the target acts on. |
| 2 | 481 |
| 482 NOTE: the column names are case sensitive and should be input exactly as they | |
| 483 are shown here. | |
| 484 | |
| 485 Example:: | |
| 486 | |
|
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487 ID Sequences Gene |
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488 Control1 TCTCGCTTGGGCGAGAGTAAG 2 |
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489 Control2 CCGCCTGAAGTCTCTGATTAA 2 |
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490 Control3 AGGAATTATAATGCTTATCTA 2 |
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491 Hairpin1 AAGGCAGAGACTGACCACCTA 4 |
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492 Hairpin2 GAGCGACCTGGTGTTACTCTA 4 |
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493 Hairpin3 ATGGTGTAAATAGAGCTGTTA 4 |
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494 Hairpin4 CAGCTCATCTTCTGTGAAGAA 4 |
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495 Hairpin5 CAGCTCTGTGGGTCAGAAGAA 4 |
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496 Hairpin6 CCAGGCACAGATCTCAAGATA 4 |
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497 Hairpin7 ATGACAAGAAAGACATCTCAA 7 |
| 2 | 498 ... |
| 499 | |
| 500 **Sample Annotation (FastQ Input):** | |
| 501 | |
| 502 A tab delimited text table of information regarding the samples. Should have | |
| 503 columns 'ID', 'Sequences' and 'group' to uniquely identify each sample, identify | |
|
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504 the sample in the reads by its sample index sequence and correctly group |
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505 replicates for analysis. Additional columns may inserted for annotation purposes |
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506 and will not interfere with analysis as long as the necessary columns are |
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507 present. |
| 2 | 508 |
|
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509 NOTE: With the exception of other_group, column names are case sensitive and |
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510 should be input exactly as they are shown here. The other_group column can be |
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511 named by the user and specified in the "Include Secondary Factor" option of the |
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512 tool. |
| 2 | 513 |
| 514 Example:: | |
| 515 | |
|
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516 ID Sequences group other_group Replicate |
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517 3 GAAAG Day 2 male 1 |
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518 6 GAACC Day 10 female 1 |
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519 9 GAAGA Day 5 GFP neg male 1 |
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520 16 GAATT Day 5 GFP pos male 1 |
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521 18 GACAC Day 2 female 2 |
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522 21 GACCA Day 10 male 2 |
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523 28 GACGT Day 5 GFP neg male 2 |
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524 31 GACTG Day 5 GFP pos female 2 |
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525 33 GAGAA Day 2 male 3 |
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526 40 GAGCT Day 10 female 3 |
| 2 | 527 ... |
| 528 | |
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529 **Include Secondary Factor** |
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530 If there are two factors involved in the experiment (i.e. Age and Gender) then |
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531 then secondary factor should be included to improve the statistical analysis. |
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532 The secondary factor should be specified as a column in the sample annotation |
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533 file and the corresponding column name should be input exactly as it is into |
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534 the provided field in the tool. |
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535 |
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536 NOTE: Currently the secondary factor is used only to improve statistical |
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537 analysis, comparisons can only be made in the primary factor specified as |
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538 "group" in the sample annotation. |
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539 |
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540 **Specify Sample Index and Target Sequence Locations (FastQ Input):** |
| 2 | 541 |
| 542 It is assumed that in the sequencing reads that the first 5 bases are the | |
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543 sample index sequence and that bases 37-57 are the hairpins/sgRNA. If this is |
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544 not the case then the values of the positions can be changed, however it still |
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545 requires the sample indices and hairpins/sgRNA to be in a consistent location an |
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546 in a continuous sequence. |
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547 |
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548 NOTE: position values start at 1 for the first base. |
| 2 | 549 |
| 550 **Filter Low CPM?:** | |
| 551 | |
| 552 Often in a large screen there may members with very low counts which are of no | |
| 553 interest in the experiment, these may be filtered out to speed up computations. | |
| 554 Filtering will be based on counts per million in a required number of samples. | |
| 555 | |
| 556 **Analysis Type:** | |
| 557 | |
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558 * **Classic Exact Test:** This allows two experimental groups to be compared |
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559 and p-values for differential representation derivec for each target |
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560 sequence. Simple and fast for straightforward comparisons. In this option you |
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561 will have the option of "*Compare* x *To* y" which implicitly subtracts the |
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562 data from y from that of x to produce the comparison. |
| 2 | 563 |
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564 * **Generalised Linear Model:** This allow for complex contrasts to be specified |
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565 and also gene level analysis to be performed. If this option is chosen then |
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566 contrasts must be explicitly stated in equations and multiple contrasts can |
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567 be made. In addition there will be the option to analyse hairpins/sgRNA on a |
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568 per-gene basis to see if hairpins/sgRNA belonging to a particular gene have |
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569 any overall tendencies for the direction of their log-fold-change. |
| 2 | 570 |
| 571 **FDR Threshold:** | |
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572 The smear plot in the output will have hairpins/sgRNA highlighted to signify |
| 2 | 573 significant differential representation. The significance is determined by |
| 574 contorlling the false discovery rate, only those with a FDR lower than the | |
| 575 threshold will be highlighted in the plot. | |
| 576 | |
| 577 ----- | |
| 578 | |
| 579 **Citations:** | |
| 580 | |
| 581 .. class:: infomark | |
| 582 | |
| 583 limma | |
| 584 | |
| 585 Please cite the paper below for the limma software itself. Please also try | |
| 586 to cite the appropriate methodology articles that describe the statistical | |
| 587 methods implemented in limma, depending on which limma functions you are | |
| 588 using. The methodology articles are listed in Section 2.1 of the limma | |
| 589 User's Guide. | |
| 590 | |
|
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591 * Smyth, GK (2005). Limma: linear models for microarray data. In: |
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592 'Bioinformatics and Computational Biology Solutions using R and |
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593 Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, |
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594 W. Huber (eds), Springer, New York, pages 397-420. |
| 2 | 595 |
| 596 .. class:: infomark | |
| 597 | |
| 598 edgeR | |
| 599 | |
| 600 Please cite the first paper for the software itself and the other papers for | |
| 601 the various original statistical methods implemented in edgeR. See | |
| 602 Section 1.2 in the User's Guide for more detail. | |
| 603 | |
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604 * Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor |
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605 package for differential expression analysis of digital gene expression |
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606 data. Bioinformatics 26, 139-140 |
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607 |
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608 * Robinson MD and Smyth GK (2007). Moderated statistical tests for assessing |
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609 differences in tag abundance. Bioinformatics 23, 2881-2887 |
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610 |
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611 * Robinson MD and Smyth GK (2008). Small-sample estimation of negative |
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612 binomial dispersion, with applications to SAGE data. |
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613 Biostatistics, 9, 321-332 |
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614 |
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615 * McCarthy DJ, Chen Y and Smyth GK (2012). Differential expression analysis |
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616 of multifactor RNA-Seq experiments with respect to biological variation. |
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617 Nucleic Acids Research 40, 4288-4297 |
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618 |
| 8 | 619 Report problems to: su.s@wehi.edu.au |
| 2 | 620 |
| 621 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html | |
| 622 .. _limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html | |
| 623 </help> | |
| 624 </tool> |