https://github.com/drpedapati/homebrew-tools
Standalone Homebrew tap for document, PDF, PubMed, PHI, and macOS CLI tools
https://github.com/drpedapati/homebrew-tools
cli document-review homebrew homebrew-tap macos phi-deidentification pubmed tools
Last synced: 2 months ago
JSON representation
Standalone Homebrew tap for document, PDF, PubMed, PHI, and macOS CLI tools
- Host: GitHub
- URL: https://github.com/drpedapati/homebrew-tools
- Owner: drpedapati
- Created: 2026-01-25T13:59:19.000Z (6 months ago)
- Default Branch: main
- Last Pushed: 2026-04-17T22:44:22.000Z (3 months ago)
- Last Synced: 2026-04-18T00:38:00.892Z (3 months ago)
- Topics: cli, document-review, homebrew, homebrew-tap, macos, phi-deidentification, pubmed, tools
- Language: Ruby
- Size: 48.8 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
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
---
## Install
```bash
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:
```bash
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:
```bash
brew install pubmed-cli docx-review pptx-review xlsx-review pdf-create pdf-form-filler phi-cleaner mac-control
```
---
## 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.**
```bash
# 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.**
```bash
# 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.**
```bash
# 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.**
```bash
# 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.**
```bash
# 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.
---
### Research & Clinical
🔬
pubmed-cli
v0.5.3
**PubMed from your terminal — search, fetch, cite, traverse.**
```bash
# 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.**
```bash
# 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.
---
### macOS
🖱️
mac-control
v0.1.0
**macOS GUI automation using the Accessibility API.**
```bash
# 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.
---
## 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.