Here are some note-taking apps which have both E2EE feature and graph:
- Anytype (Offline app): Expandable from any node while browsing
- Obsidian (Offline app): E2EE thru' plugin, not native
- Joplin (Offline app): With graph but the tree is the notebook folder tree
- Logseq (Offline app): Graph view but no tree view
- Dendron (Plugin): Not an app, a plugin for VS Code
Encrypted (E2EE) but no graph:
- LegendApp, Standard Notes, CryptPad (operates on files)
With graph but no encryption (E2EE):
- Capacities, Trillium, Roam Research
No E2EE and no graph both
- Notion, Evernote, OneNote, etc (many)
Not popular and not tried, or too simple
- Notesnook, SilentNotes, Amplenote, Supernotes, Cryptee, Turtl, DeepNotes
Pay-to-use guys
- Reflect, Roam Research
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