This question assumes a system has up-to-date package lists and packages via
apt-get update && apt-get dist-upgrade.
With the release of Raspbian PIXEL Raspbian no longer uses the standard LXDE desktop but the new PIXEL desktop. (This has somewhat different menus and tools.)
A Raspbian Lite install, which gives a text console login, can be upgraded to a graphical console and desktop with
apt-get install xserver-xorg lxde as described here and then running
raspi-config, setting "boot into Desktop" and rebooting. However, this gives the standard LXDE desktop, not the PIXEL desktop.
The introducing PIXEL post claims that one can upgrade to PIXEL with
apt-get install -y rpi-chromium-mods apt-get install -y python-sense-emu python3-sense-emu apt-get install -y python-sense-emu-doc realvnc-vnc-viewer
This brings in Chromium and some other new stuff, but even after this the system is still using the LXDE desktop. So how does one switch to the new PIXEL desktop with its new menus and so on?