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You can create images with transparent parts using either a GIF or PNG image.
In either case, go to File > Export > GIF or File > Export > PNG. You'll see a tab called Transparency.
You can make all pixels of a certain color transparent. In GIFs, check the area with "Areas that match this color" in the transparency tab. In PNGs, it's called "single color transparency." Select the color you want to be transparent, and select the tolerance. If your tolerance is one, only that exact color will be transparent, and the more you increase your tolerance by the more lax the program gets in making other colors similar to the selected color transparent.
You can also use the existing transparency and select that option if you were working with a transparent image in the first place. Just save it and you're done.
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