Chromia is supervised learning method that integrates epigenomic and genomic information to predict functional locis (e.g. promoters and enhancers) as well as TF binding sites. Chromia was proposed by Kyoung-Jae Won et al.
Genome browser is a visualization tool that can be used to view data tracks from second generation sequencing platform. AnnoJ genome browser is a web 2.0 technology based program, which provides quick response and fast readering speed. Here we provide some programs and documents that can be used to set up and configure AnnoJ genome browser on your own computer.
If you want to quickly make your data tracks can be visualized in STAR genome browser, please download software packages here. You can learn details on how to do it from README.TXT Download the data processing package
TransModis is a generalization of MODEM to consider sequence motif and multiple gene expression or ChIP-binding experiments to identify TF binding sites. Transmodis was proposed by Ron X.Yu and Jie Lie et al.