data-export-pdf_skill

Overview

This skill creates professional PDF reports locally using the reportlab library. It produces formatted text, styled tables, and embedded images or matplotlib figures and is provider-agnostic—compatible with any LLM. It is optimized for bioinformatics analysis reports like bulk, single-cell, and spatial RNA-seq summaries.

How this skill works

The skill builds a Story of platypus flowables (Paragraph, Table, Image, Spacer) and writes a PDF via SimpleDocTemplate. It accepts data objects (for example an AnnData instance or pandas DataFrame), generates summary tables and plots, saves plots as temporary images, embeds them, and optionally adds headers, footers, and multi-column layouts. Temporary files can be cleaned up after building the document.

When to use it

• Export analysis summaries and metrics for RNA-seq or multi-omics projects
• Create publication-ready supplementary materials with figures and tables
• Bundle QC reports, cluster distributions, and DEG tables into one PDF
• Produce lab reports or documentation for collaborators and reviewers
• Automate periodic report generation in local analysis pipelines

Best practices

• Choose page size (letter or A4) and set margins early in the template
• Save matplotlib figures at 150–300 DPI and remove temp files after use
• Limit table columns (4–6) and reduce font size for wide tables to fit
• Build large reports in sections to reduce memory footprint
• Use header/footer callbacks for consistent titles and page numbers

Example use cases

• Single-cell RNA-seq analysis report: dataset overview, cluster table, UMAP image
• QC report: median genes/cell,UMI stats, percent mitochondrial content as a table
• DEG summary PDF: top genes table with q-values and color-coded highlights
• Multi-sample summary: combine multiple sample metrics and comparison plots