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comparison MetaMA.xml @ 6:3ce32282f6a4 draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 228bd64b01f184d5d8ebc9f65fe0add2d45ed4fe
author sblanck
date Tue, 26 Jun 2018 08:54:45 -0400
parents 1024245abc70
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5:ca46ad51fe5a 6:3ce32282f6a4
8 <requirement type="package">bioconductor-geoquery</requirement> 8 <requirement type="package">bioconductor-geoquery</requirement>
9 <requirement type="package">bioconductor-org.hs.eg.db</requirement> 9 <requirement type="package">bioconductor-org.hs.eg.db</requirement>
10 <requirement type="package">r-venndiagram</requirement> 10 <requirement type="package">r-venndiagram</requirement>
11 <requirement type="package">r-metama</requirement> 11 <requirement type="package">r-metama</requirement>
12 <requirement type="package">r-optparse</requirement> 12 <requirement type="package">r-optparse</requirement>
13 <requirement type="package" version="1.3.3">r-upsetr</requirement>
13 </requirements> 14 </requirements>
14 15
15 <stdio> 16 <stdio>
16 <exit_code range="1:" /> 17 <exit_code range="1:" />
17 <regex match="Warning" source="both" level="warning"/> 18 <regex match="Warning" source="both" level="warning"/>
55 56
56 Given several Rdata object this tool run a meta-analysis using the metaMA R package. 57 Given several Rdata object this tool run a meta-analysis using the metaMA R package.
57 58
58 **Results** 59 **Results**
59 60
60 - Venn Diagram summarizing the results of the meta-analysis 61 - Venn Diagram or upsetR diagram (when the number of studies is greater than 2) summarizing the results of the meta-analysis
61 - A list of indicators to evaluate the quality of the performance of the meta-analysis 62 - A list of indicators to evaluate the quality of the performance of the meta-analysis
62 63
63 - DE : Number of differentially expressed genes 64 - DE : Number of differentially expressed genes
64 - IDD (Integration Driven discoveries) : number of genes that are declared differentially expressed in the meta-analysis that were not identified in any of the single studies alone 65 - IDD (Integration Driven discoveries) : number of genes that are declared differentially expressed in the meta-analysis that were not identified in any of the single studies alone
65 - Loss : Number of genes that are identified differentially expressed in single studies but not in meta-analysis 66 - Loss : Number of genes that are identified differentially expressed in single studies but not in meta-analysis