cobindR package vignette

Many transcription factors (TFs) regulate gene expression by binding to specific DNA motifs near genes. Often the regulation of gene expression is not only controlled by one TF, but by many TFs together, that can either interact in a cooperative manner or interfere with each other. In recent years high thoughput methods, like ChIP-Seq, have become available to produce large amounts of data, that contain potential regulatory regions. In silico analysis of trancription factor binding sites can help to interpret these enormous datasets in a convenient and fast way or narrow down the results to the most significant regions for further experimental studies. cobindR provides a complete set of methods to analyse and detect pairs of TFs, including support of diverse input formats and different background models for statistical testing. Several visualization tools are implemented to ease the interpretation of the results. Here we will use a case study to demonstrate how to use cobindR and its various methods properly to detect the TF pair Sox2 and Oct4. cobindR needs to be loaded together with the package Biostring, which provides methods for sequence manipulation.