Updated to version 1.0.1 in release and 1.1.1 in development (08/05/2015) 06/05/2015 Updated the vignette with sections describing how to plot average profiles. 01/05/2015 Added new colour palettes for plotting density plots. Eight different colour palettes are now available in addition to previous default palette in shades of blue. Preview of the palettes is available in the vignette. 30/04/2015 Marray package is no longer imported and, instead of the maPalette() function for creating colour palettes, the colorRampPalette() function is now used throughout. Updated to version 1.0.0 (17/04/2015) 17/04/2015 Bioconductor 3.1 release Updated to version 0.99.3 (23/03/2015) 23/03/2015 Added function plotMotifOccurrenceAverage() for plotting average profile of motif occurrence. 21/03/2015 Added function plotPatternOccurrenceAverage() for plotting average profiles of patterns occurrence. 18/03/2015 Fixed the problem of motif matching to Ns (which are assigned weights 0) when PWM has very negative values. Updated to version 0.99.2 (02/02/2015) 02/02/2015 Updated the man pages and the vignette. 01/02/2015 Adjusted the calculation of PWM score percentage for motif scanning functions to correctly calculate percentage of maximal PWM score taking into account minimal PWM score as a baseline (important when minimal score of the PWM is negative). The score threshold specified as a percentage (e.g. default value of 80%) is now converted to PWM score threshold as follows: minScore(motifPWM) + percThreshold/100 * (maxScore(motifPWM) - minScore(motifPWM)) Version 0.99.1 released in the development branch (07/01/2015)