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I know that jQuery is used as part of the WordPress core, and it comes as standard when creating a jQuery template.

I was wondering, however, if it is possible to avoid using jQuery as part of a template and use an alternative, D3, for instance?

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Yes, the scripts you use are totally up to you. Keep in mind many plugins rely on common libraries like jQuery so even if you exclude it from the theme, some of your plugins may add it back in.

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