You can obtain a word count by selecting Menu and then Word Count as demonstrated in this short video:
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This will run the texcount utility to count the words in the project's main file and any files imported into your project's main file via \include and \input. This will include references. If you do not want to include references in your word count, you can comment out the \bibliography (or similar) line and re-run the word count without the references section rendered. We are working on an update to provide an option to include references or not—we hope to have this soon.
The word counts exclude LaTeX commands and are broken down by context. Words in headers and figure captions are counted separately, which is helpful if the word counting rules you need to follow stipulate that certain words be included or excluded.
We're running the texcount utility using the following flags: -quiet -merge -incbib -dir -sub=none -utf8 -sum.