Orchestrating Microbiome Analysis with Bioconductor — article

This repository includes all the source files to used to generate article on Orchestrating Microbiome Analysis with Bioconductor. This article is written only using Quarto files, based on the Nature Quarto template.

Benchmark scripts were adapted from this separate repository which contains further details on the benchmark execution and reproducibility.

Project structure

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├── _extensions/ # Quarto extensions
├── bibliography.bib # Bibliography / references
├── data/ # Data files used in the article
├── fig.eps # EPS figure used in the manuscript
├── figures/ # Additional figures
├── manuscript.qmd # Main Quarto source file (Edit this)
├── manuscript.tex # Generated LaTeX source
├── manuscript.pdf # Rendered PDF output
├── supplementary.qmd # Supplementary material source file
├── supplementary.tex # Generated LaTeX source for supplementary material
├── supplementary.pdf # Rendered PDF output for supplementary material
├── README.md # Project documentation
├── inst/scripts # Scripts for benchmarking (Metalog data import, analysis, visualization)
├── sn-apacite.bst # BibTeX style file (APA citation style)
├── sn-aps.bst # BibTeX style file (APS style)
├── sn-basic.bst # BibTeX style file (Basic Springer style)
├── sn-chicago.bst # BibTeX style file (Chicago style)
├── sn-jnl.cls # Springer LaTeX class file
├── sn-mathphys-ay.bst # BibTeX style file (Math/Physics, author-year)
├── sn-mathphys-num.bst # BibTeX style file (Math/Physics, numeric)
├── sn-nature.bst # BibTeX style file (Nature style)
└── sn-vancouver.bst # BibTeX style file (Vancouver style)

Funding

This project received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 952914 (FindingPheno).