Meta-Analysis Manuscript Assembly

Complete systematic review and meta-analysis manuscripts for journal submission by creating publication-ready tables, figures, and references.

When to Use

• Completing meta-analysis manuscript after analyses are done

• Creating tables from meta-analysis results

• Assembling multi-panel figures from forest/funnel plots

• Generating BibTeX references for systematic reviews

• Formatting manuscripts for high-impact journals (Lancet, JAMA, NEJM)

Prerequisites

Before using this skill, ensure you have:

• Completed meta-analyses with results tables (CSV format)

• Generated individual figures (PNG at 300 DPI)

• Manuscript text sections written (Abstract, Introduction, Methods, Results, Discussion)

• List of all citations needed

Workflow

Phase 1: Tables Creation

Create comprehensive tables from analysis results:

Main Text Tables

Table 1: Trial Characteristics

• Extract from extraction.csv or similar

• Include: NCT number, first author, year, design, sample sizes, intervention details, follow-up

• Format as markdown with abbreviations section

Table 2: Efficacy Outcomes Summary

• Combine results from all meta-analyses (pCR, survival outcomes)

• Include: effect estimates, 95% CI, p-values, I², absolute benefits, NNT

• Add GRADE certainty ratings

Table 3: Safety Outcomes Summary

• From safety meta-analysis results

• Include: adverse events, rates, RR/OR, NNH

• Add clinical management guidance

Supplementary Tables

Risk of Bias Assessment

• Use RoB 2 or ROBINS-I tool format

• Domain-by-domain assessment for each trial

• Overall risk rating with justifications

GRADE Evidence Profile

• Summary of Findings table format

• All outcomes with certainty ratings

• Domain-specific justifications (bias, inconsistency, indirectness, imprecision)

Detailed Results Tables

• Individual trial results

• Subgroup analyses

• Sensitivity analyses

Phase 2: Figure Assembly

Create multi-panel publication-ready figures:

Tool: Python Script with PIL/Pillow

Create assemble_figures.py

from PIL import Image, ImageDraw, ImageFont from pathlib import Path

def add_panel_label(img, label, position='top-left', font_size=80, offset=(40, 40)): """Add A, B, C labels to panels""" draw = ImageDraw.Draw(img)

# Try to use system font
try:
    font = ImageFont.truetype("/System/Library/Fonts/Helvetica.ttc", font_size)
except:
    font = ImageFont.load_default()

x, y = offset

# Draw white background box for visibility
bbox = draw.textbbox((x, y), label, font=font)
padding = 10
draw.rectangle(
    [bbox[0] - padding, bbox[1] - padding,
     bbox[2] + padding, bbox[3] + padding],
    fill='white',
    outline='black',
    width=2
)

draw.text((x, y), label, fill='black', font=font)
return img

def create_multi_panel_figure(images_list, output_path, labels=['A', 'B', 'C'], spacing=40): """Combine multiple images vertically with labels""" # Add labels to images labeled_images = [add_panel_label(img, label) for img, label in zip(images_list, labels)]

# Calculate dimensions
max_width = max(img.width for img in labeled_images)
total_height = sum(img.height for img in labeled_images) + spacing * (len(labeled_images) - 1)

# Create combined image
combined = Image.new('RGB', (max_width, total_height), 'white')

# Paste images
y_offset = 0
for img in labeled_images:
    combined.paste(img, (0, y_offset))
    y_offset += img.height + spacing

# Save at 300 DPI
combined.save(output_path, dpi=(300, 300))
return output_path

Typical Figure Structure

Main Text:

• Figure 1: Multi-panel efficacy (pCR, EFS, OS forest plots)

• Figure 2: Subgroup analysis (e.g., by biomarker status)

• Figure 3: Safety + Publication bias (SAE forest plot, funnel plot)

Supplementary:

• Supp Figure 1: Sensitivity analyses (leave-one-out plots)

• Supp Figure 2: Publication bias (funnel plots for all outcomes)

Phase 3: References Management

Create comprehensive BibTeX file:

Steps:

Extract all citations from manuscript using grep

grep -E "¹|²|³|⁴|⁵|⁶|⁷|⁸|⁹|⁰|[\d+]" manuscript_sections.md

Create BibTeX entries for each reference

• Include DOI for all entries

• Use standardized journal abbreviations (Index Medicus)

• Format author names correctly

Create mapping document

• Map superscripts (¹, ², ³) to BibTeX keys

• Document citation locations in manuscript

Create usage guide

• Pandoc conversion instructions

• Zotero import instructions

• Manual formatting examples (Lancet, JAMA style)

Phase 4: Figure Legends

Write comprehensive legends for all figures:

Legend Structure:

Panel A. Outcome Name Description of what the panel shows. Forest plot showing [effect measure] for [outcome] across [N] trials ([total participants]). [Statistical method used]. [Key result]. Horizontal lines represent 95% confidence intervals; diamond represents pooled effect. Vertical line at [null value] indicates no treatment effect.

Abbreviations: List all abbreviations used.

Include:

• Statistical methods (random-effects, Hartung-Knapp adjustment)

• Heterogeneity measures (I², Cochran's Q)

• Clinical interpretations

• Abbreviations definitions

Phase 5: Quality Assurance

Before submission, verify:

Tables

• All data matches analysis results exactly

• Abbreviations defined

• Footnotes explain all symbols

• Column/row headers clear

• Statistical notation consistent

Figures

• All figures at 300 DPI minimum

• Panel labels (A, B, C) visible and not obscuring data

• Legends match figures exactly

• Font sizes readable (≥8pt for final print size)

• Color schemes work in grayscale

References

• All citations have corresponding references

• Reference numbers sequential

• DOIs correct and working

• Journal abbreviations standardized

• Author names match original publications

Output Structure

07_manuscript/ ├── tables/ │ ├── Table1_Trial_Characteristics.md │ ├── Table2_Efficacy_Summary.md │ ├── Table3_Safety_Summary.md │ ├── SupplementaryTable1_RiskOfBias.md │ ├── SupplementaryTable2_GRADE_Profile.md │ └── ... ├── figures/ │ ├── Figure1_Efficacy.png (300 DPI) │ ├── Figure2_Subgroup.png (300 DPI) │ ├── Figure3_Safety.png (300 DPI) │ ├── SupplementaryFigure1_Sensitivity.png │ └── ... ├── references.bib ├── FIGURE_LEGENDS.md ├── CITATION_MAPPING.md └── REFERENCES_USAGE_GUIDE.md

Time Estimates

• Tables creation: 2-3 hours

• Figure assembly: 1-2 hours

• References: 1-2 hours

• Legends: 1 hour

• QA: 1 hour

• Total: 6-9 hours

Journal-Specific Formatting

Lancet Oncology

• Word limit: 4000-5000 words

• Tables: 3-4 main text, unlimited supplementary

• Figures: 3-4 main text, unlimited supplementary

• References: Vancouver style, 30-40 typical

• Resolution: 300 DPI minimum

JAMA

• Word limit: 3500 words

• Tables: 4 max

• Figures: 4 max

• References: 40 max

• Resolution: 300-600 DPI

New England Journal of Medicine

• Word limit: 3000 words

• Tables: 3 max

• Figures: 3 max

• References: 40 max

• Resolution: 300 DPI minimum

Common Pitfalls to Avoid

• Tables: Don't mix effect measures (RR vs OR vs HR) without clear labeling

• Figures: Don't compress below 300 DPI

• References: Don't use auto-generated citations without verification

• Legends: Don't omit statistical methods or abbreviations

• Overall: Don't submit without independent verification of all numbers

Related Skills

• /meta-analysis

• Perform the statistical analyses

• /prisma-flow

• Create PRISMA flow diagram

• /grade-assessment

• Complete GRADE evidence profiles

• /risk-of-bias

• Assess trial quality with RoB 2 tool

Example Invocation

/meta-manuscript-assembly

Or with specific phase:

/meta-manuscript-assembly tables /meta-manuscript-assembly figures /meta-manuscript-assembly references

Success Criteria

• ✅ All tables publication-ready with comprehensive notes

• ✅ All figures 300 DPI with professional panel labels

• ✅ Complete BibTeX file with all 30-40 references

• ✅ Comprehensive figure legends

• ✅ All numbers verified against original analyses

• ✅ Manuscript follows target journal guidelines

• ✅ Ready for co-author review and submission