What do you mean fade in/out of the skeleton material? Do you mean the whole character/thing disappears/reappears?

If so, then yes. Every update, you can push an interpolated float 0-to-1 value to the SkeletonComponent/SkeletonAnimation's skeleton's float A field (which represents its alpha value that gets passed to the mesh which controls the transparency of all the images on that skeleton when it gets rendered).
A Spine.Skeleton also has R, G and B fields which control tinting of all parts (in addition to the tints assigned to the individual parts) if you want to affect that too.

Pharan is right of course, but note that a skeleton usually uses a number of images that overlap slightly, so when changing the alpha of all images you can often see the overlap.