R package for anlaysis of ChIP-seq and other functional sequencing data * Assess overall DNA-binding signals in the data and select appropriate quality of tag alignment. * Discard or restrict positions with abnormally high number of tags. * Calculate genome-wide profiles of smoothed tag density and save them in WIG files for viewing in other browsers. * Calculate genome-wide profiles providing conservative statistical estimates of fold enrichment ratios along the genome. These can be exported for browser viewing, or thresholded to determine regions of significant enrichment/depletion. * Determine statistically significant point binding positions * Assess whether the set of point binding positions detected at a current sequencing depth meets saturation criteria, and if does not, estimate what sequencing depth would be required to do so.