To rotate the picture clockwise you can use the rotate filter, indicating a positive angle in radians. With 90 degrees equating with PI/2, you can do it like so:
ffmpeg -i in.mp4 -vf "rotate=PI/2" out.mp4
for counter-clockwise the angle must be negative
ffmpeg -i in.mp4 -vf "rotate=-PI/2" out.mp4
The transpose filter will work equally well for 90 degrees, but for other angles this is a faster or only choice.