CopywriteR is widely applicable. (A) Sample T97 (FFPE) was subjected to WES, and copy number profiles relative to C41 (fresh frozen reference material) are displayed for onTarget and CopywriteR methods, with segmentation values (CBS) depicted in red (left panel: whole-genome; right panel: chromosome 9). (B, left panel) ChIPseq data were obtained from ChIP experiments on the MCF7 cell line with the indicated set of antibodies, or from the relevant input control. Copy number data were extracted using CopywriteR, and further analyzed employing CBS. Segmentation values are represented as a heatmap. (B, right panel) Data were analyzed as for the left panel. ChIPseq data were obtained from ChIP experiments on ER+ breast cancer with ER-antibodies (E), or from the relevant input (I) control. (C, left panel) A set of matched pre- and post-vemurafenib treatment melanoma samples were subjected to targeted sequencing on a 1,977-gene panel. Copy number information was extracted using CopywriteR and example regions of the resulting copy number profiles are presented, with segmentation values (CBS) depicted in red. (C, right panel) Segmentation values were plotted as a heatmap for the pre/post-treatment pairs.