EdgeR results file, tab seperated consist the columns [enzyme logFC logCPM PValue FDR association].
After a file is uploaded, a new section appears, enables the selection of the control and the experiment treatments.
The selection of control and experiment treatments drives the calculatin of basic statistics which are now shown.
Entities number in a pathway: select a range of minimum and maximum number of entities linked with a pathway in the enrichment analysis.
The selection of the range above a drives the enrichment analysis calculation and a new option is then enabled -
Select pathways to dropout: select which pathways to drop out of the network.
Environmental resource node color: select the color of the compounds which are essential for the network to develop (seeds).
Unique node color: select the color of the compounds which are differential abunded due to the treatment.
Limit node hubness: Select the maximum allowed number of connected edges to a node.
Set network layout iterations: NetworkX network layout itterations. Higher number would produce arranged network, but consume more time to calculate (up to few minutes).
A dual set of results would be produced, one for each treatment, consists the following files: