This is potentially a very interesting and useful tool. The most important factor in whether is is useful is how the normalisation is done. You state:
> Heatmaps represent Pearson’s correlation values between experiments calculated using a Gene x Experiment numeric matrix with normalised gene expression values for expression data, a Genomic regions x Experiments binary matrix indicating presence or ab- sence of a peak for TF ChIP-seq data and a Genomic re- gions x Experiments numeric matrix of expression values for CAGE data.
Can you please expand on this, giving detail about the expression normalisation and representation used for RNAseq and CAGE, and how peak calls are normalised for ChIP-seq. Adding this explanation to the text would, in my opinion, help users feel confident in the tool.