diff --git a/conf/test.config b/conf/test.config index a32b096e..676dfe64 100644 --- a/conf/test.config +++ b/conf/test.config @@ -47,4 +47,5 @@ params { // Activate gprofiler2 gprofiler2_run = true + gprofiler2_organism = 'mmusculus' } diff --git a/docs/images/workflow.png b/docs/images/workflow.png index daa0858f..21bb9011 100644 Binary files a/docs/images/workflow.png and b/docs/images/workflow.png differ diff --git a/docs/images/workflow.svg b/docs/images/workflow.svg index 81ef5b14..ab379a62 100644 --- a/docs/images/workflow.svg +++ b/docs/images/workflow.svg @@ -2,9 +2,9 @@ + y="348.19925" /> + y="331.51535" /> + x="111.85512" + y="288.01227" /> + + id="tspan5453"> getGEO + id="tspan5455">getGEO + id="tspan5457"> justRMA + id="tspan5459">justRMA + id="tspan5461"> readProteinGroups + id="tspan5463">readProteinGroups GTF to + id="tspan5465">GTF to table + id="tspan5467">table Validate + id="tspan5469">Validate Limma + id="tspan5471">Limma GSEA + id="tspan5473">GSEA gprofiler2 + id="tspan5475">gprofiler2 DESeq2 + id="tspan5477">DESeq2 Filter matrix + id="tspan5479">Filter matrix - + y="391.19058" /> + y="391.10669" /> GEO ID + id="tspan5481">GEO ID Maxquant + id="tspan5483">Maxquant output + id="tspan5485">output Affy + id="tspan5487">Affy intensities + id="tspan5489">intensities Reference + id="tspan5491"> Reference annotation + id="tspan5495">annotation Contrast + id="tspan5499">Contrast definitions + id="tspan5501">definitions @@ -1165,11 +1164,11 @@ y="0">Feature + id="tspan5503">Feature annotations + id="tspan5505">annotations Abundance + id="tspan5507">Abundance values + id="tspan5509">values Observation + id="tspan5511">Observation annotations + id="tspan5513">annotations + + + + + + - Plot exploratory + id="tspan5515">Plot exploratory Plot differential + id="tspan5517">Plot differential + R Markdown notebook @@ -1559,24 +1594,24 @@ inkscape:export-xdpi="90" inkscape:export-filename="./polygon4618.png" id="text3362-8-6" - y="345.41769" + y="378.22653" x="112.9056" style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:6.35px;line-height:1.35;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro';display:inline;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.264583" xml:space="preserve">Build Shiny app TSV - + + + + + +