wes-clinical-report-en

Convert WES markdown reports into English clinical PDFs with pharmacogenomics analysis.

Updated May 10, 2026

Search Tags:#bioinformatics #PDF generation #pharmacogenomics #clinical report #WES

Ready to run

npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill wes-clinical-report-en

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: wes-clinical-report-en
Source: https://github.com/MubasherMohammed/opencode-BioInfo/tree/main/python/skills/wes-clinical-report-en
Command: npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill wes-clinical-report-en

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires reportlab, pandas, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

This Skill automatically generates English-language clinical reports from WES data, eliminating manual reporting work.

Core Features & Use Cases

Professional Reporting: Converts WES markdown reports into structured, formatted clinical PDF reports with clinical interpretations and follow-up recommendations.
Clinical Interpretation: Incorporates pathogenic variant identification, pharmacogenomics analysis, and rare damaging variant prioritization.
Customizable Layout: Supports configurable institutional logos on covers and headers. Adaptable for Novogene or custom WES data.

Quick Start

To generate a WES clinical report for all samples in 'Reports/' and save it in 'PDF-EN/', use:

python skills/wes-clinical-report-en/wes_clinical_report_en.py --report-dir /path/to/Reports/ --output-dir /path/to/PDF-EN/

Frequently Asked Questions about wes-clinical-report-en

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I automate WES clinical report generation from markdown files?▼

Automate WES clinical report generation by running a Python script that converts markdown reports into formatted English clinical PDFs, processing all samples in a specified directory and outputting them to a target folder.

What is included in a pharmacogenomics clinical report for whole exome sequencing data?▼

A pharmacogenomics clinical report for whole exome sequencing includes pathogenic variant identification, pharmacogenomics analysis, rare damaging variant prioritization, clinical interpretations, and follow-up recommendations.

Do I need pandas and reportlab to generate clinical PDF reports from WES data?▼

Yes, you need pandas and reportlab installed, as they are required dependencies for data manipulation and structured PDF generation when converting WES markdown files into clinical reports.

Can I add institutional logos to the headers of WES clinical PDF reports?▼

Yes, the layout is customizable and supports configurable institutional logos on both the report cover and headers to adapt the WES clinical PDF output for specific organizations.

Does this clinical report generation tool work with Novogene WES data?▼

Yes, the clinical report generation tool is adaptable and explicitly supports processing WES markdown data from Novogene or custom sources to produce professional English PDF reports.

What is the best way to convert multiple WES markdown reports into PDFs at once?▼

The best way to convert multiple WES markdown reports is using the command line interface, where you specify the input report directory and output folder to batch process all samples automatically.