cobindR detects pairs of transcription factor binding sites. Its focus is ease of use, rigorous statistical testing, and good visualization.
Transcription factors (TFs) can regulate gene expression by binding to specific DNA motifs near genes. Moreover, gene expression can be controlled by combinations of TFs, which either cooperate or interfere with each other. High thoughput methods, like ChIP-Seq, are available to indicate large numbers of potential regulatory regions. In silico analysis of trancription factor binding sites (TFBS) helps to interprete datasets or to narrow down the results for further experimental studies.
- easy parameter documentation via configuration files
- easy data input via diverse input formats
- different background models for statistical testing
- various intuitive result visualizations
- export results via diverse formats