== Using ngsplot to make stacked heatmaps and profiles of genes or genomic regions (like ChIP-seq peaks) ==
 [[https://github.com/shenlab-sinai/ngsplot | ngsplot]] is a great tool to make heatmaps and profiles of mapped reads (i.e. bam files of RNA-seq, ChIP-seq etc) across genes, transcription starts sites or other regions of interest.