From Markdown Syntax Overview :
For any markup that is not covered by Markdowns syntax, you simply use HTML. Theres no need to preface it or limit it to indicate that you are switching from Markdown to HTML; you just use tags.
I am sure that there is a better way to include scripts in your project, but if you really want to incorporate them into your markdown, there should be nothing to stop you from doing the following:
# This is a title > this is a blockquote <script> </script>
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