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
-
+
+
+
+
+
+