In Bio7 it is possible to write a documentation in knitr. A simple visual and textual HTML editor (based on JavaFX) and an embedded Latex editor (based on TeXclipse) helps in the creation of a *.html or *.pdf documentation. For the *.pdf creation a TeX environment has to be available (Windows e.g. MiKTeX).
Note that there is still a bug in the visual JavaFX HTML editor (JavaFX SWT bug) to select text in the visual part of the editor. A workaround is to use the combination of Shift- or Ctrl-key and a mouse-click.
In upcoming releases more improvements for R reports will be available in Bio7.