You don't need a package to construct an MA plot. Any plotting software will do. You simply have to create your x (the A part of the MA plot) and y (the M part) components appropriately. The purpose of the MA plot is to view a ratio of two things, as a function of the magnitude of those same two things. Thus if you have two things you'd like to compare, i.e. wt and mut, you create a ratio:

y = log2(mut/wt)

and for the x-axis you combine wt and mut to get a magnitude (geometric mean):

x = log2(sqrt(wt*mut))

Then you simply plot x against y. You could do it in excel, or R, or whatever - the package doesn't matter. The components of what you are plotting matter. MA plots simply make a nice way to view large numbers of ratios.