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meta_analysis_brohee

Meta-analysis of diet effects on the Periplaneta americana gut microbiome. Includes raw data, R scripts for effect-size calculation (Hedges’ g, log-RR), mixed-effects models, and reproducible forest, funnel & sensitivity plots.

https://github.com/mzb0226/meta_analysis_brohee

Science Score: 67.0%

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    Links to: zenodo.org
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    Low similarity (11.3%) to scientific vocabulary
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Repository

Meta-analysis of diet effects on the Periplaneta americana gut microbiome. Includes raw data, R scripts for effect-size calculation (Hedges’ g, log-RR), mixed-effects models, and reproducible forest, funnel & sensitivity plots.

Basic Info
  • Host: GitHub
  • Owner: mzb0226
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 462 KB
Statistics
  • Stars: 0
  • Watchers: 1
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Created 10 months ago · Last pushed 10 months ago
Metadata Files
Readme Citation

README.md

Meta-Analysis Repository

Welcome to my repository!
My name is Muhtarin Khayer Brohee, and I am a Ph.D. student in the Department of Biological Sciences at Auburn University.

This repository was created as part of my class (FISH-7350) project and manuscript titled:
"The Influence of Diet on the Gut Microbiome of Periplaneta americana (American Cockroach): A Meta-Analysis."

Project Overview

This meta-analysis systematically evaluates how dietary interventions affect the gut microbiota of Periplaneta americana, focusing on: - Changes in alpha diversity (Shannon Index) - Phylum-level shifts in Firmicutes and Bacteroidetes proportions - The Firmicutes:Bacteroidetes (F:B) ratio

Effect sizes were calculated using Hedges' g for alpha diversity and log response ratios (log RR) for relative abundance data. A random-effects meta-analysis model was applied using the metafor package in R, with heterogeneity assessments (I², tau², Q-statistic) performed following REML estimation. The analysis adhered to PRISMA guidelines for systematic reviews and meta-analyses.

Repository Contents

  • Data/ – Raw and processed data files
  • Scripts/ – R scripts for:
    • Effect size calculations
    • Random-effects meta-analysis
    • Forest plots, funnel plots, and leave-one-out sensitivity analyses
  • Plots/ – Publication-ready figure files (PNG, PDF)
  • Results/ – Excel summary tables and PDF outputs
    • Forest plots for alpha diversity and taxonomic outcomes
    • Funnel plots to assess publication bias
    • Leave-one-out (LOO) plots for sensitivity analysis
  • Supplementary/ – Supplementary figures (S1–S12) and tables (S1–S2)
  • Reference/ – EndNote library files for citation management

Software and Environment

  • R version: 4.4.2
  • Key R packages:
    • metafor (v4.8-0)
    • readxl (v1.4.3)
    • dplyr (v1.1.4)
    • ggplot2 (v3.4.4)
    • writexl (v1.4.2)
    • orchaRd (v2.0)
    • devtools (v2.4.5)

Acknowledgments

The author gratefully acknowledges the support and guidance of Dr. Alan Wilson for providing essential materials and mentorship throughout this project. Special thanks to Auburn University librarians Adelia Grabowsky and Patricia Hartmen for their expertise in literature searching and data acquisition. Additional gratitude goes to all classmates for their constructive feedback and discussions. Finally, thanks to ChatGPT for assistance with script debugging and optimization.

Citation

If you use this github project/script in your research, please cite it as: Muhtarin Khayer Brohee. (2025). mzb0226/MetaanalysisBrohee: v1.0.0 – The Influence of Diet on the Gut Microbiome of Periplaneta americana (American Cockroach): A Meta-Analysis (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.15306932

DOI

Owner

  • Login: mzb0226
  • Kind: user

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it using the following metadata."
title: "The Influence of Diet on the Gut Microbiome of Periplaneta americana (American Cockroach): A Meta-Analysis"
version: "v1.0.0"
date-released: "2025-04-29"
authors:
  - family-names: "Brohee"
    given-names: "Muhtarin Khayer"
repository-code: "https://github.com/mzb0226/Meta_analysis_Brohee"
url: "https://doi.org/10.5281/zenodo.15306932"

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