Research themes

A research theme is one Markdown note per piece of work. Send quotes and highlights into it from many papers, with their sources, arrange them under headings, and export the result to start writing. Every quote can take you back to its place in the paper.

Applies to Mendeley and Zotero editions Windows · Mac · iPad Partly included in the purchase

Create or open a theme

  • Mac · iPadPress the light bulb in the reader's toolbar, or press ⌘⇧T. Without a paper open, choose … › Research theme in the library.
  • iPadOn iPhone and in a narrow window, choose … › Research theme in the reader.
  • WindowsClick Research theme (with the light bulb) in the bar at the top. Once a theme is chosen, the button shows Theme: name, and clicking it opens the theme beside the paper.

The first time, choose New theme…, type a name and press Create. A new theme starts with the headings Questions, Claims, Evidence, Objections, Open questions and Inbox. You can keep them, rename them or add your own.

To switch to another theme, make a new one, rename or delete the current one:

  • Mac · iPadUse the theme's name at the top of the theme, and its … menu (Rename theme…, Delete theme…).
  • WindowsUse the arrow next to the Research theme button. It also has Open a note as a theme… (any .md file) and Show the themes folder.
Mac · iPad

Where there is room, the light bulb shows the theme as a column beside the paper; otherwise it opens as a sheet. In the sheet, the beside-the-paper button (Show beside the paper) moves it into the column.

Creating, arranging and exporting themes is free. Showing a theme beside the paper (the column on iPad and Mac, the second pane on Windows) is included in the purchase; it is free during the 14-day trial and beside the sample paper. On iPad and Mac, sending to a theme stays free because it works without the column; on Windows, sending needs the theme open beside the paper.

Send passages to the theme

  1. Select text in a paper, in the PDF view or in Reading Mode.
  2. Choose Send to theme:
    • Mac · iPadIn the menu that appears over the selection, or in the menu of a highlight you tap. On Mac, also by right-clicking. The shortcut is ⌘⇧N.
    • WindowsIn the bar that appears over the selection, by right-clicking, or with Ctrl+Shift+N. The theme (or another note) must be open beside the paper.
  3. The passage is added to the current theme as a quotation, followed by its source: the paper's citation key and page, such as [@devlin2019bert, p. 5]. A highlight's note comes along below the quotation.
  • Mac · iPadIt always goes to the current theme, even when the theme is not on screen. "Added to “name”" confirms it. With no theme yet, Rectoly asks you to create one first.
  • By default, passages go under Inbox. To send them under another heading:
    • Mac · iPadIn the theme's … menu, choose Where in the note and a heading (Under …) or At the end.
    • WindowsClick the arrow next to Send to theme and choose Under … or At the end. The choice is kept for that note.
  • The form of the source follows the citation key format in Settings. See Citation key format.

Arrange the theme

The theme shows as an outline: headings you can fold, and under them the blocks you sent.

  • WindowsSwitch the note between Text and Outline above it, or press Ctrl+Shift+O. In the text view you edit the Markdown directly.
  • Drag a block to move it, or use a block's menu to Move to another heading, Edit it or Delete it.
  • Mac · iPadSelect a block and press ⌥↑ / ⌥↓ to move it.
  • WindowsSelect a block and press Alt+↑ / Alt+↓ to move it.
  • Add a heading with Heading (choose a suggested one or Other…).
  • Show in the paper on a block opens the paper at the place the quotation came from (Return / Enter on a selected block).

Export and write

  • Copy as Markdown puts the whole theme on the clipboard.
  • Export › Markdown file… or Word (.docx)… saves it as a file.
    • Mac · iPadBoth are in the theme's … menu.

What goes out is clean Markdown: headings you never used are left out, Rectoly's own markers are removed, and a References list of the papers you quoted is added at the end.

Where themes are kept

A theme is a plain Markdown file, name.md, that you can also open in other apps.

  • When a notes folder is set, themes are kept in its Themes folder. iPad, Mac and Windows all use this place.
  • Mac · iPadWithout a notes folder, themes are kept inside the app. When you choose a notes folder, they move into its Themes folder.
  • WindowsWithout a notes folder, themes are kept in Documents\Rectoly\Themes.
  • Mac · iPadIf the same theme was changed in two places, a banner says "This theme was changed in two places." Choose which version to keep; sending pauses until you do.
  • WindowsIf another app changed the note, Rectoly asks which version to keep before you send again.

Updated September 20, 2026