homebrew-tools

CLI tools for document review, scientific research, clinical data, and macOS automation.
Built for humans and AI agents. One tap, eight tools.

Use drpedapati/tap for sciClaw itself. Use drpedapati/tools when you want the standalone tools directly.

Install • Tools • Office Suite • Research • macOS

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Install

brew tap drpedapati/tools

This tap is for standalone utilities. It is intentionally separate from the main sciClaw tap:

• drpedapati/tap installs sciclaw, sciclaw-dev, irl, and sciclaw-* companion formulas
• drpedapati/tools installs the standalone tools listed below
• deprecated legacy tap: drpedapati/sciclaw (users should untap it if still present)

Then install any tool:

brew install pubmed-cli        # PubMed search & literature synthesis
brew install docx-review       # Word tracked changes & comments
brew install pptx-review       # PowerPoint editing & comments
brew install xlsx-review       # Excel editing & comments
brew install pdf-create        # PDF generation from JSON
brew install pdf-form-filler   # AcroForm inspection and fill
brew install phi-cleaner       # Clinical text de-identification
brew install mac-control       # macOS GUI automation

Or install everything:

brew install pubmed-cli docx-review pptx-review xlsx-review pdf-create pdf-form-filler phi-cleaner mac-control

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Tools

Document Office Suite

Programmatic document editing via JSON manifests. Read, edit, comment — all from the command line. Built with .NET 8 and Open XML SDK. Cross-platform (macOS, Linux). Designed so AI agents can review and modify Office documents without ever opening Word, PowerPoint, or Excel.

📝 docx-review v1.1.0	Add tracked changes and comments to Word documents. # Read existing review state docx-review paper.docx --read --json # Apply tracked changes from a JSON manifest docx-review paper.docx edits.json -o paper_reviewed.docx # Pipe from stdin cat edits.json | docx-review paper.docx --author "Reviewer 1" # Dry run (validate without modifying) docx-review paper.docx edits.json --dry-run Insert, delete, replace text with full revision tracking. Add margin comments anchored to specific text. All changes appear in Word's Review pane exactly as if a human reviewer made them.
📊 pptx-review v1.0.1	Edit and comment on PowerPoint presentations. # Read slide contents pptx-review deck.pptx --read --json # Apply edits from manifest pptx-review deck.pptx edits.json -o deck_edited.pptx # Validate changes without writing pptx-review deck.pptx edits.json --dry-run Edit text, add speaker notes, insert comments — all driven by JSON. Review presentations programmatically without opening PowerPoint.
📈 xlsx-review v1.0.0	Edit Excel spreadsheets with highlighted changes and comments. # Read spreadsheet contents xlsx-review data.xlsx --read --json # Apply edits with change highlighting xlsx-review data.xlsx edits.json -o data_edited.xlsx # Add comments to cells cat edits.json | xlsx-review data.xlsx --author "Data Review" Cell edits, formula updates, comments, formatting — highlight changes so reviewers can see exactly what was modified.
📄 pdf-create v1.0.0	Generate PDFs from JSON manifests. # Generate a PDF from a manifest pdf-create report.json -o report.pdf # Pipe from stdin cat manifest.json | pdf-create -o output.pdf --json Describe your document layout in JSON — headings, paragraphs, tables, images, page breaks — and get a pixel-perfect PDF. Built on QuestPDF. Ideal for automated report generation.
🧾 pdf-form-filler v0.1.0	Inspect and fill real AcroForm PDFs from the command line. # Inspect a PDF form pdf-form-filler inspect --pdf prior-auth.pdf --json # Export a stable field schema pdf-form-filler schema --pdf prior-auth.pdf # Fill from JSON while keeping the result editable for human review pdf-form-filler fill --pdf prior-auth.pdf --values values.json --out filled.pdf --json # Flatten only for final non-editable output pdf-form-filler fill --pdf prior-auth.pdf --values values.json --out final.pdf --flatten Designed for true AcroForm workflows with stable schema export, JSON-driven fill, encrypted form handling, and optional flattening for final distribution.

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Research & Clinical

🔬 pubmed-cli v0.5.3

PubMed from your terminal — search, fetch, cite, traverse. # Search PubMed pubmed search "fragile X syndrome EEG" --max 10 # Fetch full article details pubmed fetch 39906041 --json # Citation traversal pubmed cited-by 39906041 # Who cited this? pubmed references 39906041 # What does this cite? pubmed related 39906041 # Similar articles # Literature synthesis with APA citations pubmed synth "FMRP and synaptic plasticity" # Interactive wizard pubmed wizard # Answer biomedical questions with adaptive retrieval pubmed qa "Does CBD improve seizures in Dravet syndrome?" Zero dependencies. Structured JSON output. Agent-ready. Includes pubmed synth for AI-powered literature synthesis with proper APA citations and RIS export. Built for both terminal power users and AI coding agents.

🏥 phi-cleaner v0.1.0

De-identify clinical text using BERT-based NER models. # De-identify inline text phi-clean "Patient John Smith was seen on 03/15/2024 at Mayo Clinic." # → Patient [PATIENT] was seen on [DATE] at [HOSPITAL]. # Process a file phi-clean -f clinical_note.txt -o cleaned.txt # Batch process a directory phi-clean -d ./notes/ -O ./cleaned/ # Detection only (no replacement) phi-clean --detect "Dr. Chen ordered labs for MRN 12345678" # Choose replacement style phi-clean --redact "..." # [REDACTED] phi-clean --generic "..." # [PATIENT], [DATE], etc. phi-clean --underscores "..." # _____ Detects patient names, provider names, dates, hospitals, IDs/MRNs, phone numbers, and vendor names. Uses StanfordAIMI/stanford-deidentifier-base (BERT NER). Runs locally — no data leaves your machine.

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macOS

🖱️ mac-control v0.1.0

macOS GUI automation using the Accessibility API. # List clickable elements in an app mac-ui list "Finder" # Click by element index or coordinates mac-ui click 5 mac-control click 100 200 # Type text and press keys mac-control type "Hello, world" mac-control key "cmd+space" # Take a screenshot mac-control screenshot Two commands: mac-control for direct mouse/keyboard input and mac-ui for Accessibility-based element discovery and interaction. Requires macOS Accessibility permissions.

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Platform Support

Tool	macOS (ARM)	macOS (Intel)	Linux (ARM)	Linux (x86)
pubmed-cli	✅	✅	—	—
docx-review	✅	✅	✅	✅
pptx-review	✅	✅	✅	✅
xlsx-review	✅	✅	✅	✅
pdf-create	✅	✅	✅	✅
phi-cleaner	✅	✅	✅	✅
mac-control	✅	✅	—	—

License

All tools are MIT licensed. See individual repositories for details.