Five apps for one paper
A reference manager, a PDF reader, a notes app, a citation tool and a chatbot. Copying between them is half the work.
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New: Papyr 1.0.0 for Windows, macOS & Linux
Papyr Read, note, cite and write. All connected.
Papyr is a reference manager, PDF reader, notebook and thesis workspace in one offline app. Your highlights flow into your notes, your notes cite your papers, and Papyr shows you the papers you are missing. Ask your library questions and get answers that point to the page.
Free No account, no trial, no catch
- Windows, macOS & Linux
- Works offline
- Your files, your folder
- AI optional, local or cloud
- Apps it replaces
- 5
- Citation styles built in
- 7
- AI providers to choose from
- 11
- Accounts needed
- 0
Research, scattered
Your research lives in five apps that don't talk to each other.
Reading, highlighting, note-taking, citing, finding papers and writing are one job. Papyr treats them as one, so every highlight, note and citation knows where it came from.
Highlights that go nowhere
You marked the key sentence months ago. Finding it again, and the page it came from, takes longer than reading it twice.
02The paper you didn't know about
Your sources keep citing a classic you never saved, and a new study on your exact topic came out last month.
03A thesis held together by hope
Chapters in one place, citations in another, deadlines in your head, and a bibliography rebuilt by hand before every draft.
04Collect, read, take notes
Your papers and your thinking, in the same place.
A proper reference manager, a fast PDF reader and a Markdown notebook, built as one app so nothing gets lost between them.
Library
A reference manager that stays out of your way.
Drop in PDFs, import from Zotero, BibTeX or RIS, or paste a DOI. Papyr fills in the details, gives every paper a stable citation key, and keeps the files in a folder you can open without it.
- Drag and drop PDFs; the DOI is read from the first page and details are fetched for you
- Import Zotero exports, BibTeX, RIS and CSL JSON, with their PDFs; export BibTeX, RIS and CSL JSON
- Tags, nested collections, reading status and saved searches
- Duplicates found by DOI and title, and merged without losing highlights or notes
Search
Search inside every PDF and note at once.
Type a phrase and see where it appears: in a paper's details, on page 7 of a PDF, or in your own notes, with the words highlighted. Click a result and the reader opens on that page.
- Full-text search across PDFs, notes, and the text of slides, documents and data files
- Results show the page and a snippet with your words marked
- Search by meaning too: find passages about an idea even when the words differ
- Works offline, and stays fast with thousands of papers
Reader and notes
Highlight a sentence. It lands in your notes, linked to the page.
Every paper has its own Markdown note, open beside the PDF. Highlights and figure snips are added to it automatically, each with a link that jumps back to the exact spot.
- Text highlights in colours you give meaning to, with comments
- Snip a figure or table as an image straight into your note
- Links between notes, backlinks, tags and templates, like Obsidian; open your existing Obsidian vault too
- Cite with @key as you write; references format in APA, Chicago, Harvard, IEEE, MLA, Nature, Vancouver or any CSL style
More than PDFs
Data, slides, figures and web pages, kept with the paper.
Attach any file to a paper and Papyr shows it: tables you can filter, images you can zoom, code and notebooks, slide decks and documents as readable text. Their contents are searchable too.
- CSV and TSV as tables, images with zoom, text and code with line numbers, Jupyter notebooks with their outputs
- Word, PowerPoint, Excel, OpenDocument and EPUB files read as text; open the original any time
- Save a web page as an offline copy, shown without scripts or trackers
- Audio and video play in place; anything else opens in its usual app
AI that cites its sources
Ask your library. Get answers that point to the page.
Papyr answers from your own papers and notes, never from the open web, and shows exactly where each claim comes from. Run it on your computer, or bring your own key for a cloud model.
Questions and summaries
Every claim with a source you can open.
Ask a question across your whole library, a collection or a single paper. The answer cites numbered sources; click one and the PDF opens on that page.
- Answers built only from passages in your papers and notes
- Each source names the paper and page, and opens the reader there
- Summarise a paper in a click and keep the summary in its note
- Before anything goes to a cloud model, you see what will be sent
Local or cloud, your choice
Private on your laptop, or the strongest model with your key.
Use Ollama or LM Studio to keep everything on your computer, or connect Claude, ChatGPT, Gemini, Mistral, OpenRouter, Groq, DeepSeek, Grok or any compatible server with your own API key.
- Off by default; Papyr works fully without AI
- Cloud providers need your explicit consent before they are switched on
- API keys stored in your system's keychain, never in files
- Search by meaning uses embeddings from the provider you pick, kept on your device
Find what you are missing
See the literature around your papers.
Papyr follows citations outward from what you have already read, so the important papers you have not saved yet stand out, and new work in your area finds you.
Citation maps
Start from one paper. See the whole conversation.
Pick a paper, a few, or a collection. Papyr gathers what they cite, what cites them and what is often cited alongside them, ranks them by how closely they connect, and lays them out by year and citations.
- Each paper says why it is there: cited by your seeds, cites them, or cited alongside them
- Papers you already have are filled in; the rest are one click from your library
- Use any paper as another seed, or mark it not relevant
- Maps are saved in your library and open offline
Discover
Suggestions for your whole library, with the reason why.
Papyr looks across your library, a collection or the papers a thesis cites, and lists the papers that keep coming up but are not saved yet.
- Foundations your papers cite, new work that cites them, and related papers
- Labels like "Cited by 8 of your papers" and "Linked to Smith 2021"
- Filter by year, sort by match, citations or date
- Add straight into the collection you are looking at
New papers
Hear about new papers in your area.
Watch a citation map or a list of suggestions, and Papyr checks now and then for newly published papers that cite them. They arrive in an inbox, each saying which of your papers it cites.
- Daily, weekly or monthly, only while Papyr is open, and only after you turn it on
- Only paper identifiers are sent, nothing from your notes or PDFs
- Add, open, mark read or dismiss in a click
- A count in the sidebar when something new arrives
Share a map
Put a map in your slides, or send it to your supervisor.
Export a map as a sharp picture, an interactive web page anyone can open, or a reference file for any other tool.
- PNG and SVG pictures with a title, axes and a legend
- One HTML file with hover, click and links, no install needed
- BibTeX or RIS with full details for every paper
- Export the map as shown, all of it, or only the papers you have not saved
Write the thesis
From notes to a finished chapter, without the bookkeeping.
Chapters are notes, citations are live, and progress, gaps and deadlines are tracked for you.
Thesis mode
Chapters, word targets and a bibliography that builds itself.
Arrange chapters, set word targets and a deadline, and watch progress day by day. When it is time to submit, export the whole thesis with formatted citations.
- Word counts per chapter and in total, with a daily pace to your deadline
- Export to Word, PDF, LaTeX (with biblatex), HTML or Markdown with BibTeX
- Your citation style applied everywhere, with a warning for keys not in your library
- Chapter status from draft to done
Literature review tables
Compare papers side by side, filled from your highlights.
Choose columns like aim, method, data and findings. Papyr fills them from highlights of matching colours or comments, and AI can draft the empty cells for you to check.
- Every cell links back to the highlight and page it came from
- AI drafts stay marked until you accept or edit them
- Export to Word, CSV, HTML or Markdown
- Add papers from anywhere in your library
Gaps
What is waiting for you, with the next step.
Papyr notices papers saved but never opened, read but never noted, highlighted but never cited, reading that stalled, chapters falling behind and collections nobody has started.
- Each item comes with an action: read next, write a note, copy the citation, resume
- Chapters under half their target, or long with hardly any citations
- Collections where nothing has been read yet
- Checks your library on your computer; nothing is sent anywhere
Timeline
Deadlines, milestones, meetings and tasks on one line.
Your thesis deadline and milestones, supervisor meetings, and every task you wrote in a note as a checkbox, grouped into overdue, this week and the months ahead.
- Tick a task here and the checkbox in your note updates
- Dates written naturally in notes are picked up
- Add milestones in a click
- Past months and finished items tucked away until you want them
Graph
See how your papers and notes connect.
An interactive graph of papers and notes, linked by citations and note links. Spot the papers nothing points to, and focus on a thesis, collection or tag.
- Papers coloured by reading status, notes as squares
- Click a node to see its connections, double-click to open it
- Filter by thesis, collection, tag or status
- Highlights unlinked papers in one click
Cite while you write · Word on Windows
Your Papyr library, inside Microsoft Word.
Writing in Word? The Papyr add-in puts your library beside your document. Search, pick, insert, and the citations and bibliography format themselves.
The Papyr pane in Word
Search, pick, insert. The bibliography keeps up.
The same citation styles and the same papers as in Papyr, so a citation reads the same in your notes and in your chapter.
- Search your Papyr library from a pane beside your document
- Cite one paper or several at once, with page numbers, "see" and "for a review"
- A bibliography in your citation style, updated as you write
- Numbered styles renumber themselves as you add and remove citations
- Pick a different style for one document without changing your library
- Your own edits to a citation are kept, never silently overwritten
- Turn everything into plain text for the final version
- Works with Papyr on your computer; nothing goes online
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Turn on the connection in Papyr
Click W in Papyr's title bar and tick "Let Word connect to Papyr". It only listens on your own computer.
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Add Papyr to Word
Download the add-in file below. At work, your IT team can add it for everyone from the Microsoft 365 admin center (Integrated apps). On your own PC, put it in a shared folder, add that folder in Word under File, Options, Trust Center, Trusted Add-in Catalogs, then pick Papyr from Home, Add-ins, Shared Folder. A one-click listing in Microsoft's add-in store is on its way.
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Connect and cite
In Word, click Papyr on the Home tab, then Connect, and allow it in Papyr after checking the code matches.
For Word in Microsoft 365 or Word 2021 and later, on Windows 10 and 11. Needs Papyr open on the same PC. Not yet available for Word on Mac or Word on the web.
The full list
Everything Papyr does.
The features above, and all the small things that make a research tool pleasant to live in.
Library
- Add PDFs by drag and drop or file picker
- DOI read from the PDF; details from Crossref, OpenAlex, Semantic Scholar and Europe PMC
- Identify a paper from a DOI, arXiv ID, PubMed ID, BibTeX or its title
- Import Zotero, BibTeX, RIS and CSL JSON with attached files
- Export BibTeX, RIS and CSL JSON
- Stable, editable citation keys that never change silently
- Tags, collections, reading status and saved searches
- Duplicate detection and safe merging
Finding PDFs
- Free, legal copies from OpenAlex, Unpaywall, Europe PMC, arXiv, bioRxiv, medRxiv and CORE
- Sign in through your university library (EZproxy or Shibboleth) in a built-in window
- A ready-to-send email asking the author for a copy
- A link to your library's interlibrary loan page
Reading
- Fast PDF reader with outline, zoom and find
- Text highlights in colours, with comments
- Figure and table snips as images
- Page-level reading progress, marked read at 90%
- Reading queue and a weekly reading goal
- Open in your own PDF app any time
Notes
- Markdown notes with live preview
- A note for every paper, with its highlights kept in sync
- Wiki links, backlinks, tags, folders and templates
- LaTeX maths and code blocks
- Open an Obsidian vault without changing it
- Edit notes in any other editor; Papyr keeps up
Citing and writing
- @key citations with autocomplete
- APA, Chicago, Harvard, IEEE, MLA, Nature and Vancouver built in, plus any CSL style
- Thesis chapters, word targets, deadline and daily pace
- Export to Word, PDF, LaTeX, HTML or Markdown with BibTeX
- A Word add-in to cite while you write (Word on Windows)
- Literature review tables from highlights
- Renaming a paper or note updates every link to it
AI (optional)
- Ask questions with page-level sources
- One-click summaries saved to the note
- Search by meaning across papers and notes
- AI drafts for review tables, always marked
- Ollama and LM Studio on your computer
- Claude, ChatGPT, Gemini, Mistral, OpenRouter, Groq, DeepSeek, Grok and compatible servers
Discovery
- Citation maps by year and citations
- Suggestions for the library, a collection or a thesis
- New-paper alerts for maps and suggestions
- Export maps as PNG, SVG, interactive HTML, BibTeX or RIS
- Data from OpenAlex, free and open
Planning
- Gaps: what to read, note and cite next
- Timeline of deadlines, milestones, meetings and tasks
- Graph of papers and notes
- Any file type attached to a paper, and searchable
Your data
- A plain folder of PDFs and Markdown you can open without Papyr
- Automatic backups every six hours, the last ten kept
- Deleted files go to a trash folder, never erased
- Export everything as a zip in one click
- Works offline; nothing goes online unless you ask
- Windows, macOS and Linux, in light and dark
Private by design
Your research stays yours.
- Your files, your folderYour library is a normal folder of PDFs and Markdown notes. Open it with any app, back it up any way you like.
- No account, works offlineThere is nothing to sign up for. Reading, notes, search and writing all work without the internet.
- Online only when you askLooking up details, finding PDFs, building maps and AI only go online when you use them, and only with what they need.
Papyr vs the usual stack
One app where there used to be five.
The usual stack: a reference manager, a notes app, a discovery service, a chatbot and a word processor.
| Task | The usual stack | Papyr |
|---|---|---|
| Save and organise papers | A reference manager | Built in |
| Highlights in your notes | Copy and paste, plus a plugin | Automatic, linked to the page |
| Notes that cite papers | A separate notes app | Same app, @key citations |
| Questions about your papers | A chatbot that can't see them | Answers from your library, with pages |
| Papers you are missing | A separate discovery service | Citation maps and suggestions from your library |
| New papers in your area | Email alerts per service | An inbox for what you watch |
| Citations in Word | A plugin per reference manager | The Papyr add-in, straight from your library |
| Thesis progress and export | Word counts by hand | Targets, pace and one-click export |
| Who holds your data | Several companies' servers | A folder on your computer |
Get Papyr
Your whole research workflow, in one app.
Pick the file for your system. We'll email you a one-time code, and the download starts as soon as you enter it.
Windows
Windows 10 and 11, 64-bit
macOS
macOS 11 Big Sur or later
Linux
64-bit (x86_64)
First launch
Windows
If Windows shows "Windows protected your PC", choose More info, then Run anyway. On Windows 10, the installer adds Microsoft's WebView2 if it's missing.
macOS
Drag Papyr into Applications. The first time, open System Settings, then Privacy & Security, and click Open Anyway. (On macOS 14 and earlier, right-click the app and choose Open.) If macOS says Papyr is damaged, run xattr -dr com.apple.quarantine /Applications/Papyr.app once.
Linux
Install the .deb with apt or the .rpm with dnf, like any other package. The AppImage needs no install: make it executable (chmod +x) and run it.
Word add-in
Install Papyr first, then add Papyr to Word as described in the Word section above. Word on Windows only.
The first-launch warning appears because Papyr is new and not yet widely downloaded; it only shows once. Verify your download (optional): each file's SHA-256 checksum is in SHA256SUMS.txt.
FAQ
Questions, answered.
Something else? Ideas or feedback? Email jamal@unravelers.tech.
Who is Papyr for?
Anyone who reads a lot of papers and writes something long from them: PhD students and postdocs first, and also master's students, academics and researchers in industry.
Can I bring my Zotero, Mendeley or EndNote library?
Yes. Import a Zotero export (with your PDFs), or BibTeX and RIS from Mendeley, EndNote and most other tools. Your Obsidian vault can be opened as it is.
Do I need the AI features?
No. Papyr is complete without them, and AI stays off until you switch it on. When you do, you choose a model on your computer or a cloud provider with your own key.
Does my data leave my computer?
Only when you use an online feature: looking up a paper's details, finding a PDF, building a citation map, checking for new papers, or a cloud AI provider. Each sends only what it needs, and cloud AI always asks first.
Does it work with Word?
Yes, on Windows. The Papyr add-in for Word searches your library and inserts citations and a bibliography in your citation style as you write, talking only to Papyr on your computer. The add-in isn't available for Word on Mac or Word on the web yet. On any system, Papyr can export a whole thesis to Word.
What happens if I stop using Papyr?
Nothing is lost. Your PDFs, notes and highlights are ordinary files in your folder, and you can export your references as BibTeX, RIS or CSL JSON at any time.
When can I download it?
Now, from the download section above.
Which systems are supported?
Windows 10 and 11 (64-bit), macOS 11 or later on Apple silicon and Intel, and 64-bit Linux (Ubuntu, Debian, Fedora, openSUSE and others).
Read, note, cite and write
Spend your time on research, not on bookkeeping.
Papyr for Windows, macOS and Linux. Free, offline, and yours.