Global analysis
Library size	MDS plot	Box plot of normalized signals

Individual Contrasts analysis
Volcano plots	Significant Changed Genes	MA plots	Heatmap TopHits	Heatmap TopHits, High Fold
Differential Expression Each Contrast	Differential Expression All Contrasts

Experiment Analysis
Correlation matrix of Experiments	Heatmap of Experiments	Gene Network Significant Changed Genes	Gene Network High Fold Changed Genes
Clustering Median FOLD k-means	Clustering High FOLD k-means	Clustering Mean SIGNALS k-means	Dendrogram Median Fold k-means	Dendrogram High Fold k-means

Analysis of the Classes
k-means RATIO Class TopHits	k-means SIGNAL Class TopHits	Mean SIGNAL Plots Each Class	Correlation matrix All Classes	Correlation matrices Each Class
Heatmap Class TopHits	Heatmap Class Signals	Heatmaps Each Class	MDS plot of k-means of ClassTophits

Data tables
Link to file	Description
Class TopHits ClusterIDs	Table of Class TopHits and there ClusterID
Class TopHits High Fold	Table of Class HighFold: Fold Change > 5, p-value < 0.01
Class TopHits logFC	Table of Class and Log2 Fold Change values. TopHits= Fold Change > 5 and p-value<0.05
Class TopHits mean signals	Table of Class TopHits Signals
Contrasts Overview	Overview of COntrasts and link to TopHits tables of each Contrast
Correlation Matrix Classes	Correlation between Class members over Experiments
Correlation Matrix Experiments	Correlation between Experiments
Differential Expression all Contrasts	DE table, all values
Differential Expression all Contrasts logFC	DE table TopHits= Fold Change > 2 and p-value<0.05
Differential Expression all Contrasts logFC High Fold	DE table High Fold: Fold Change > 5, p-value < 0.01
Filenames in JSON format	Summery JSON formmated file with filenames for downstream processing
Filenames of Class TopHits k-means	Overview of k-means clusters
Filenames of Correlation Matrix of Classes	Filenames
Filenames of Heatmaps Class TopHits	File with filenames of all heatmaps of each Class group
Filenames of MA Plots	Filenames
Filenames of Mean Signals Classes	Mean Signals of Genes
Filenames of Mean Signals Classes log2	Filenames
Filenames of Mean signals Classes TopHits	Mean Signals of Genes
Filenames of Significant changed Genes	Complete table with Significant changed genes
Filenames of Volcano Plot data	Filenames
Filenames of k-means High Fold	Filenames
Filenames of k-means on Fold change	Filenames
Gene Network Edges	Gene network for Cytoscape of Changed genes
Gene Network Edges High Fold	Gene network for Cytoscape of HighFold Changed genes
Heatmap of Class Signals	Heatmap of Class Signals
Heatmap of Class Tophits	Heatmap of Class TopHits
Heatmap of Experiments	Heatmap of Experiments
Heatmap of High Fold Tophits	Heatmap of HighFold TopHits of all Contrasts
Heatmap of Tophits	Heatmap of TopHits of all Contrasts
Mean signals log2	Log2 Signals normalized
Mean signals log2 Scaled	Log2 Signals Global scaled
Mean signals log2 Scaled per Class	Log2 Signals Scaled per Class
Mean signals log2 Scaled per Gene	Log2 Signals Scaled per Gene
Mean signals of replicates	Mean Signal of replicates
Normalised Data Table	Normalized data
k-means High Fold ClusterIDs	k-means Cluster IDs
k-means on Fold change ClusterIDs	Table with Cluster IDs