The rapid raise and use of genome-wide techniques raises the need for the development of computational and bioinformatics tools to integrated and comparative analysis of genomic data. To this end, we have developed two computational tools, TFARM and ChroKit, designed for the integrated analysis of chromatin modifications and transcription factors binding. TFARM is a suite that uses novel algorithms based on association rules and ranking metrics driven by the definition of an Importance index, to infer functional and physical association of transcription factors, thus providing information on transcription factors networks and transcription factories. Chrokit is multiplatform software with an advanced graphical interface which provides intuitive and efficient tools for the analysis of genomic data from ChIP-seq, RNA-seq and other similar techniques.