Changes in version 2024.1.24 - reformat NEWS. - fix man pages for CRAN. Changes in version 2017.08.15 - remove binSum. - add cDPA_interface. Changes in version 2017.06.20 - depend on penaltyLearning, delete related code in this pkg. Changes in version 2016.08.06 - Suggest ggplot2 >= 2.0, new geom_tallrect implementation. - cDPA C code now computes total Poisson loss which is consistent with the PoissonLoss R function, and with other packages (Segmentor3IsBack, coseg). It has been significantly cleaned up (duplication removed). Changes in version 2015.04.07 - move joint segmentation code to PeakSegJoint package. Changes in version 2015.04.02 - multiSampleSegZoom C function. - R implementation of multiSampleSegSome. Changes in version 2015.03.27 - Scripts up to Step4 under exec/ Changes in version 2015.03.23 - Error checking in binSum. - chrom and sample ratio features in exec/Step1.R Changes in version 2015.03.16 - multiSampleSeg Optimal and Heuristic C code. Changes in version 2015.03.11 - clusterPeaks C code. - LinDynProg.c renamed to cDPA to be consistent with paper. Changes in version 2015.03.05 - Do not use GSL headers for positive infinity cost; instead use INFINITY defined in "math.h" Changes in version 2015.03.03 - fista.R interval regression code. - binSum C code sets count to -1 for profiles that are too short for the number of bins requested. Changes in version 2015.02.27 - binSum C code for quickly computing sums over bins of constant size. Changes in version 2014.11.10 - warning when user requests X peaks but that model is infeasible.