1. cisTarget: target gene prediction based on detection of homotypic clusters combined with network-level conservation of these clusters in Drosophila melanogaster.
  2. cisTargetX: extension of the cisTarget framework to incorporate expression profiles, enabling the prediction of motifs that explain a set of co-expressed genes in Drosophila melanogaster. Moreover, the subset of the co-expressed signature that is directly controlled by an enriched motif is provided.
  3. i-cisTarget: the latest tool in the suite. An integrative genomics method for the prediction of regulatory features and cis-regulatory modules in Drosophila melanogaster.