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SQLiteStudio
A free, open source, multi-platform SQLite database manager
...You can Ctrl+click on the table mentioned in the SQL query to open that table (or index, or trigger, or view). Currently supported encrypted, password-protected SQLite variations are SQLCipher, WxSQLite3, and System.Data.SQLite. You can execute SQL statements that refer to multiple databases within a single query, thanks to a transparent database attaching mechanism built into the SQL Editor of SQLiteStudio. You can implement your own SQL functions (scalar & aggregate) using JavaScript, Python, or Tcl. There is a repository of ready-to-use scripts on the wiki page.
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