Added code to circle nested bin pair on rotated plot. Interweaved code into list of steps in quick start. Reworded reporting of nested results. Minor rewordings elsewhere.
Added book chapter citation for edgeR.
Reworded alignment comment, added comment about read processing already been done for Sofueva.
Added comment boxes to the start of each chapter, reworded some references to filtering chapter. Fiddled with some formatting to avoid excess pages.
Added section on data sources in the epilogue.