Introduction | Workflow of the package | CNE identification | CNE visualisation | Input | axt alignment file | Filtering information | Creating a CNE class | Scan axt alignments | Merge CNEs | Realignment of CNEs | CNE storage and query | CNE length distribution | Genomic distribution of CNEs along the chromosome | Output of bed and bedGraph files | CNEs visualisation | Gene annotation visualisation | CNEs horizon plot | Conclusions | References

Introduction | S4 classes in TFBSTools | XMatrix and its subclasses | XMatrixList and its subclasses | SiteSet, SiteSetList, SitePairSet and SitePairSetList | MotifSet | TFFM and its subclasses | Database interfaces for JASPAR2014 database | Search JASPAR2014 database | Store, delete and initialize JASPAR2014 database | PFM, PWM and ICM methods | PFM to PWM | PFM to ICM | Align PFM to a custom matrix or IUPAC string | PWM similarity | Dynamic random profile generation | TFFM methods | The graphical representation of TFFM | Scan sequence and alignments with PWM pattern | searchSeq | searchAln | searchPairBSgenome | Use de novo motif discovery software | MEME | Session info | References

Introduction | Prerequisite | Aligning | LASTZ aligner | last aligner | YASS aligner | Chaining: | Netting: | axtNet | Session info