annotate edgeR.xml @ 4:e0e1518e56f6 draft

Uploaded
author rouan
date Thu, 26 Dec 2013 05:35:56 -0500
parents 22c941d89a89
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
22c941d89a89 Uploaded
rouan
parents:
diff changeset
1 <tool id="edgeR" name="edgeR" version="0.0.2">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
2 <description> - Estimates differential gene expression for short read sequence count using methods appropriate for count data</description>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
3 <requirements>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
4 <requirement type="R-module">edgeR</requirement>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
5 <requirement type="R-module">limma</requirement>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
6 </requirements>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
7 <command interpreter="perl">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
8 edgeR.pl -a $analysis_type.analysis -e $html_file.files_path -f $fdr -h $html_file -o $output
22c941d89a89 Uploaded
rouan
parents:
diff changeset
9 ## Pairwise comparisons
22c941d89a89 Uploaded
rouan
parents:
diff changeset
10 #if $analysis_type.analysis == "pw":
22c941d89a89 Uploaded
rouan
parents:
diff changeset
11 -r $analysis_type.rowsumfilter
22c941d89a89 Uploaded
rouan
parents:
diff changeset
12 #if $analysis_type.tagwise_disp.twd == "TRUE":
22c941d89a89 Uploaded
rouan
parents:
diff changeset
13 -u $analysis_type.tagwise_disp.twd_trend
22c941d89a89 Uploaded
rouan
parents:
diff changeset
14 -t
22c941d89a89 Uploaded
rouan
parents:
diff changeset
15 #end if
22c941d89a89 Uploaded
rouan
parents:
diff changeset
16 ## GLM
22c941d89a89 Uploaded
rouan
parents:
diff changeset
17 #else if $analysis_type.analysis == "glm":
22c941d89a89 Uploaded
rouan
parents:
diff changeset
18 #if $analysis_type.exp.export_norm == "true":
22c941d89a89 Uploaded
rouan
parents:
diff changeset
19 -n $norm_exp
22c941d89a89 Uploaded
rouan
parents:
diff changeset
20 #end if
22c941d89a89 Uploaded
rouan
parents:
diff changeset
21 -d $analysis_type.disp
22c941d89a89 Uploaded
rouan
parents:
diff changeset
22 $analysis_type.cont_pw
22c941d89a89 Uploaded
rouan
parents:
diff changeset
23 #for $fct in $analysis_type.factors:
22c941d89a89 Uploaded
rouan
parents:
diff changeset
24 factor::${$fct.fact_name}::${$fct.fact}
22c941d89a89 Uploaded
rouan
parents:
diff changeset
25 #end for
22c941d89a89 Uploaded
rouan
parents:
diff changeset
26 #for $c in $analysis_type.cont_pred:
22c941d89a89 Uploaded
rouan
parents:
diff changeset
27 cp::${c.cp_name}::${c.cp}
22c941d89a89 Uploaded
rouan
parents:
diff changeset
28 #end for
22c941d89a89 Uploaded
rouan
parents:
diff changeset
29 #for $cnt in $analysis_type.contrasts:
22c941d89a89 Uploaded
rouan
parents:
diff changeset
30 "cnt::${cnt.add_cont}"
22c941d89a89 Uploaded
rouan
parents:
diff changeset
31 #end for
22c941d89a89 Uploaded
rouan
parents:
diff changeset
32 ## LIMMA
22c941d89a89 Uploaded
rouan
parents:
diff changeset
33 #else
22c941d89a89 Uploaded
rouan
parents:
diff changeset
34 #if $analysis_type.exp.export_norm == "true":
22c941d89a89 Uploaded
rouan
parents:
diff changeset
35 -n $norm_exp $analysis_type.exp.log
22c941d89a89 Uploaded
rouan
parents:
diff changeset
36 #end if
22c941d89a89 Uploaded
rouan
parents:
diff changeset
37 $analysis_type.cont_pw
22c941d89a89 Uploaded
rouan
parents:
diff changeset
38 #for $fct in $analysis_type.factors:
22c941d89a89 Uploaded
rouan
parents:
diff changeset
39 factor::${$fct.fact_name}::${$fct.fact}
22c941d89a89 Uploaded
rouan
parents:
diff changeset
40 #end for
22c941d89a89 Uploaded
rouan
parents:
diff changeset
41 #for $c in $analysis_type.cont_pred:
22c941d89a89 Uploaded
rouan
parents:
diff changeset
42 cp::${c.cp_name}::${c.cp}
22c941d89a89 Uploaded
rouan
parents:
diff changeset
43 #end for
22c941d89a89 Uploaded
rouan
parents:
diff changeset
44 #for $cnt in $analysis_type.contrasts:
22c941d89a89 Uploaded
rouan
parents:
diff changeset
45 "cnt::${cnt.add_cont}"
22c941d89a89 Uploaded
rouan
parents:
diff changeset
46 #end for
22c941d89a89 Uploaded
rouan
parents:
diff changeset
47 #end if
22c941d89a89 Uploaded
rouan
parents:
diff changeset
48 $matrix
22c941d89a89 Uploaded
rouan
parents:
diff changeset
49
22c941d89a89 Uploaded
rouan
parents:
diff changeset
50 </command>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
51
22c941d89a89 Uploaded
rouan
parents:
diff changeset
52 <inputs>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
53 <param name="matrix" type="data" format="tabular" label="Digital Expression Matrix"/>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
54 <conditional name="analysis_type">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
55 <param name="analysis" type="select" label="Type Of Analysis">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
56 <option value="pw">Pairwise comparisons (1 Factor Analysis)</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
57 <option value="glm" selected="true">Generalized Linear Models (Multiple Factor Analysis using GLM)</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
58 <option value="limma">Linear Models for RNA-Seq (Multiple Factor Analysis using LIMMA)</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
59 </param>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
60 <when value="pw">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
61 <param name="rowsumfilter" type="integer" value="5" label="Common Dispersion Rowsum Filter" help="Numeric scalar giving a value for the filtering out of low abundance tags in the estimation of the common dispersion. Only tags with total sum of counts above this value are used in the estimation of the common dispersion. Low abundance tags can adversely affect the estimation of the common dispersion, so this argument allows the user to select an appropriate filter threshold for the tag abundance."/>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
62 <conditional name="tagwise_disp">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
63 <param name="twd" type="select" label="Maximize the Negative Binomial Weighted Conditional Likelihood" help="Calculate and use an estimate of the dispersion parameter for each tag">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
64 <option value="TRUE" selected="true">True</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
65 <option value="FALSE">False</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
66 </param>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
67 <when value="TRUE">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
68 <param name="twd_trend" type="select" label="Method for allowing the prior distribution for the dispersion to be abundance-dependent">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
69 <option value="movingave" selected="true">Movingave</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
70 <option value="tricube">Tricube</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
71 <option value="none">None</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
72 </param>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
73 </when>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
74 </conditional>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
75 </when>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
76 <when value="glm">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
77 <param name="disp" type="select" label="Select The Dispersion Estimate To Use:">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
78 <option value="common">Common Dispersion</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
79 <option value="trend">Trended Dispersion</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
80 <option value="tag" selected="true">Tagwise Dispersion</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
81 </param>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
82 <repeat name="factors" title="Factor">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
83 <param name="fact_name" title="Factor Name" type="text" label="Name Of Factor (no spaces or commas)"/>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
84 <param name="fact" title="Factor" type="text" size="100" label="The Level Of Each Sample Seperated By A Colon (no spaces or commas)"/>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
85 </repeat>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
86 <repeat name="cont_pred" title="Continuous Predictor">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
87 <param name="cp_name" title="Continuous Predictor Name" type="text" label="Name Of Continuous Predictor (no spaces or commas)"/>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
88 <param name="cp" title="Continuous Predictor" type="text" size="100" label="The Numerical Value For Each Sample Seperated By A Colon (no spaces or commas)"/>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
89 </repeat>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
90 <param name="cont_pw" type="boolean" truevalue="-m" falsevalue="" checked="True" label="Perform all pairwise comparisons" help="Include all pairwise comparisons in the contrast matrix."/>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
91 <repeat name="contrasts" title="Contrast">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
92 <param name="add_cont" title="Contrast" type="text" label="Enter the contrast of interest, e.g. (G1+G2)/2-G3 (no spaces or commas)"/>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
93 </repeat>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
94 <conditional name="exp">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
95 <param name="export_norm" type="select" label="Save Normalised DGE Matrix">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
96 <option value="true">Yes</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
97 <option value="false">No</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
98 </param>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
99 </conditional>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
100 </when>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
101 <when value="limma">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
102 <repeat name="factors" title="Factor">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
103 <param name="fact_name" title="Factor Name" type="text" label="Name Of Factor (no spaces or commas)"/>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
104 <param name="fact" title="Factor" type="text" size="100" label="The Level Of Each Sample Seperated By A Colon (no spaces or commas)"/>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
105 </repeat>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
106 <repeat name="cont_pred" title="Continuous Predictor">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
107 <param name="cp_name" title="Continuous Predictor Name" type="text" label="Name Of Continuous Predictor (no spaces or commas)"/>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
108 <param name="cp" title="Continuous Predictor" type="text" size="100" label="The Numerical Value For Each Sample Seperated By A Colon (no spaces or commas)"/>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
109 </repeat>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
110 <param name="cont_pw" type="boolean" truevalue="-m" falsevalue="" checked="True" label="Perform all pairwise comparisons" help="Include all pairwise comparisons in the contrast matrix."/>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
111 <repeat name="contrasts" title="Contrast">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
112 <param name="add_cont" title="Contrast" type="text" label="Enter the contrast of interest, e.g. (G1+G2)/2-G3 (no spaces or commas)"/>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
113 </repeat>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
114 <conditional name="exp">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
115 <param name="export_norm" type="select" label="Save Normalised DGE Matrix">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
116 <option value="true">Yes</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
117 <option value="false">No</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
118 </param>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
119 <when value="true">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
120 <param name="log" type="boolean" truevalue="-l" falsevalue="" checked="True" label="Export Normalised DGE Matrix in Log2" help="Selecting this will log base 2 transform the Normalised Digital Gene Expression Matrix."/>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
121 </when>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
122 </conditional>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
123 </when>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
124 </conditional>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
125 <param name="fdr" type="select" label="False discovery rate adjustment method">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
126 <option value="BH">Benjamini and Hochberg (1995)</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
127 <option value="holm">Holm (1979)</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
128 <option value="hochberg">Hochberg (1988)</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
129 <option value="hommel">Hommel (1988)</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
130 <option value="BY">Benjamini and Yekutieli (2001)</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
131 <option value="none">None</option>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
132 </param>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
133 </inputs>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
134
22c941d89a89 Uploaded
rouan
parents:
diff changeset
135 <outputs>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
136 <data format="tabular" name="output" label="EdgeR analysis on ${matrix.name}"/>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
137 <data name="html_file" format="html" label="EdgeR analysis plots for ${matrix.name}"/>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
138 <data name="norm_exp" format="tabular" label="EdgeR Norm Expr Matrix for ${matrix.name}">
22c941d89a89 Uploaded
rouan
parents:
diff changeset
139 <filter>analysis_type[ "analysis" ] != "pw" and analysis_type[ "exp" ][ "export_norm" ] == "true"</filter>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
140 </data>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
141 </outputs>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
142
22c941d89a89 Uploaded
rouan
parents:
diff changeset
143 <help>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
144
22c941d89a89 Uploaded
rouan
parents:
diff changeset
145 .. class:: infomark
22c941d89a89 Uploaded
rouan
parents:
diff changeset
146
22c941d89a89 Uploaded
rouan
parents:
diff changeset
147 **What it does**
22c941d89a89 Uploaded
rouan
parents:
diff changeset
148
22c941d89a89 Uploaded
rouan
parents:
diff changeset
149 Estimates differential gene expression for short read sequence count using methods appropriate for count data.
22c941d89a89 Uploaded
rouan
parents:
diff changeset
150 If you have paired data you may also want to consider Tophat/Cufflinks.
22c941d89a89 Uploaded
rouan
parents:
diff changeset
151 Input must be raw count data for each sequence arranged in a rectangular matrix as a tabular file.
22c941d89a89 Uploaded
rouan
parents:
diff changeset
152 Note - no scaling - please make sure you have untransformed raw counts of reads for each sequence.
22c941d89a89 Uploaded
rouan
parents:
diff changeset
153
22c941d89a89 Uploaded
rouan
parents:
diff changeset
154 Performs digital differential gene expression analysis between groups (eg a treatment and control).
22c941d89a89 Uploaded
rouan
parents:
diff changeset
155 Biological replicates provide information about experimental variability required for reliable inference.
22c941d89a89 Uploaded
rouan
parents:
diff changeset
156
22c941d89a89 Uploaded
rouan
parents:
diff changeset
157 **What it does not do**
22c941d89a89 Uploaded
rouan
parents:
diff changeset
158 edgeR_ requires biological replicates.
22c941d89a89 Uploaded
rouan
parents:
diff changeset
159 Without replicates you can't account for known important experimental sources of variability that the approach implemented here requires.
22c941d89a89 Uploaded
rouan
parents:
diff changeset
160
22c941d89a89 Uploaded
rouan
parents:
diff changeset
161
22c941d89a89 Uploaded
rouan
parents:
diff changeset
162 **Input**
22c941d89a89 Uploaded
rouan
parents:
diff changeset
163 A count matrix containing sequence names as rows and sample specific counts of reads from this sequence as columns.
22c941d89a89 Uploaded
rouan
parents:
diff changeset
164 The matrix must have 2 header rows, the first indicating the group assignment and the second uniquely identifiying the samples. It must also contain a unique set of (eg Feature) names in the first column.
22c941d89a89 Uploaded
rouan
parents:
diff changeset
165
22c941d89a89 Uploaded
rouan
parents:
diff changeset
166 Example::
22c941d89a89 Uploaded
rouan
parents:
diff changeset
167
22c941d89a89 Uploaded
rouan
parents:
diff changeset
168 # G1:Mut G1:Mut G1:Mut G2:WT G2:WT G2:WT
22c941d89a89 Uploaded
rouan
parents:
diff changeset
169 #Feature Spl1 Spl2 Spl3 Spl4 Spl5 Spl6
22c941d89a89 Uploaded
rouan
parents:
diff changeset
170 NM_001001130 97 43 61 34 73 26
22c941d89a89 Uploaded
rouan
parents:
diff changeset
171 NM_001001144 25 8 9 3 5 5
22c941d89a89 Uploaded
rouan
parents:
diff changeset
172 NM_001001152 72 45 29 20 31 13
22c941d89a89 Uploaded
rouan
parents:
diff changeset
173 NM_001001160 0 1 1 1 0 0
22c941d89a89 Uploaded
rouan
parents:
diff changeset
174 NM_001001177 0 1 0 4 3 3
22c941d89a89 Uploaded
rouan
parents:
diff changeset
175 NM_001001178 0 2 1 0 4 0
22c941d89a89 Uploaded
rouan
parents:
diff changeset
176 NM_001001179 0 0 0 0 0 2
22c941d89a89 Uploaded
rouan
parents:
diff changeset
177 NM_001001180 0 0 0 0 0 2
22c941d89a89 Uploaded
rouan
parents:
diff changeset
178 NM_001001181 415 319 462 185 391 155
22c941d89a89 Uploaded
rouan
parents:
diff changeset
179 NM_001001182 1293 945 987 297 938 496
22c941d89a89 Uploaded
rouan
parents:
diff changeset
180 NM_001001183 5 4 11 7 11 2
22c941d89a89 Uploaded
rouan
parents:
diff changeset
181 NM_001001184 135 198 178 110 205 64
22c941d89a89 Uploaded
rouan
parents:
diff changeset
182 NM_001001185 186 1 0 1 1 0
22c941d89a89 Uploaded
rouan
parents:
diff changeset
183 NM_001001186 75 90 91 34 63 54
22c941d89a89 Uploaded
rouan
parents:
diff changeset
184 NM_001001187 267 236 170 165 202 51
22c941d89a89 Uploaded
rouan
parents:
diff changeset
185 NM_001001295 5 2 6 1 7 0
22c941d89a89 Uploaded
rouan
parents:
diff changeset
186 NM_001001309 1 0 0 1 2 1
22c941d89a89 Uploaded
rouan
parents:
diff changeset
187 ...
22c941d89a89 Uploaded
rouan
parents:
diff changeset
188
22c941d89a89 Uploaded
rouan
parents:
diff changeset
189
22c941d89a89 Uploaded
rouan
parents:
diff changeset
190 Please use the "Count reads in features with htseq-count" tool to generate the count matrix.
22c941d89a89 Uploaded
rouan
parents:
diff changeset
191
22c941d89a89 Uploaded
rouan
parents:
diff changeset
192 **Output**
22c941d89a89 Uploaded
rouan
parents:
diff changeset
193
22c941d89a89 Uploaded
rouan
parents:
diff changeset
194 A tabular file containing relative expression levels, statistical estimates of differential expression probability, R scripts, log, and some helpful diagnostic plots.
22c941d89a89 Uploaded
rouan
parents:
diff changeset
195
22c941d89a89 Uploaded
rouan
parents:
diff changeset
196 .. class:: infomark
22c941d89a89 Uploaded
rouan
parents:
diff changeset
197
22c941d89a89 Uploaded
rouan
parents:
diff changeset
198 **Attribution**
22c941d89a89 Uploaded
rouan
parents:
diff changeset
199 This tool wraps the edgeR_ Bioconductor package so all calculations and plots are controlled by that code. See edgeR_ for all documentation and appropriate attribution.
22c941d89a89 Uploaded
rouan
parents:
diff changeset
200 Recommended reference is Mark D. Robinson, Davis J. McCarthy, Gordon K. Smyth, PMCID: PMC2796818
22c941d89a89 Uploaded
rouan
parents:
diff changeset
201
22c941d89a89 Uploaded
rouan
parents:
diff changeset
202 .. class:: infomark
22c941d89a89 Uploaded
rouan
parents:
diff changeset
203
22c941d89a89 Uploaded
rouan
parents:
diff changeset
204 **Attribution**
22c941d89a89 Uploaded
rouan
parents:
diff changeset
205 When applying the LIMMA (Linear models for RNA-Seq) anlysis the tool also makes use of the limma_ Bioconductor package.
22c941d89a89 Uploaded
rouan
parents:
diff changeset
206 Recommended reference is Smyth, G. K. (2005). Limma: linear models for microarray data. In: 'Bioinformatics and Computational Biology Solutions using R and Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds), Springer, New York, pages 397--420.
22c941d89a89 Uploaded
rouan
parents:
diff changeset
207
22c941d89a89 Uploaded
rouan
parents:
diff changeset
208 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
22c941d89a89 Uploaded
rouan
parents:
diff changeset
209 .. _limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html
22c941d89a89 Uploaded
rouan
parents:
diff changeset
210
22c941d89a89 Uploaded
rouan
parents:
diff changeset
211
22c941d89a89 Uploaded
rouan
parents:
diff changeset
212 </help>
22c941d89a89 Uploaded
rouan
parents:
diff changeset
213
22c941d89a89 Uploaded
rouan
parents:
diff changeset
214 </tool>