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jasonrec, welcome on the XOOPS forum!
Which XOOPS, module, editor version are you using?
Some editors must be configured to allow the script tag, because it is in general a security risk if users can add JavaScript to your site.
It is a bad practice to mingle Javascript with content. It is better to group the required functions in a file and to add a reference for this in the theme file.
Then you can add the functions to the onclick or other events.
What kind of code do you want to use?
If it is for RSS feeds there are modules for that (see module repository).