Slicer lets you rotate STLs around the Z axis with its Plater/45ccw|45cw|rotate buttons.
Netfabb lets you rotate around X,Y or Z with its rotate tool.
To use these tools to rotate a part from horizontal to vertical, you could open it in Netfab, rotate 90 degrees around X or Y, export it as STL, then open the new file in slicer.