This repository contains the analysis pipeline, data, and source code for the metaWGCNA framework: a co-expression analysis of metatranscriptomics to understand organic micropollutants degradation in complex microbiomes. This study applies Weighted Gene Co-expression Network Analysis (WGCNA) to analyze metatranscriptomics and metagenomics from single-omics and multi-omics perspectives at the module level. The main purpose is to understand Organic Micropollutant (OMP) degradation rates in wastewater microbiomes.
- Metatranscriptomics WGCNA: Identify co-expression modules from taxonomic groups and correlate them with OMP degradation rates.
- Metagenomics WGCNA: Analyze taxonomic abundance co-occurrence modules and correlate them with OMP degradation.
- Cross-Omics Integration: Correlate eigengenes from transcript modules with taxonomic modules.
- Functional Enrichment: Perform enrichment analysis (KEGG/NOGs) for modules significantly correlated with degradation.
metaWGCNA/
├── analysis.Rmd
├── data/
│ ├── raw_counts/
│ │ └── 2024-10-01_spades_transcript_counts.csv
│ ├── metadata/
│ │ ├── clusters.tsv
│ │ ├── coverm_drep-relative_abundances.tsv
│ │ └── nitrosomonas_kbios.csv
│ └── enrichment/
│ ├── gtdbtk.bac120.summary.tsv
│ └── out.bin.all.emapper.annotations.zip
├── images/
│ ├── illustrations/
│ └── results/
└── README.md
- Edir Vidal: Methodology and software development (R), and bioinformatics analysis (gene-set enrichment analysis, cross-omics correlations, etc.).
- Michaël Pierrelée: Data curation and normalization, guidance on the downstream analyses and statistical validation.
- Alberto Santos Delgado: Conceptualization and guidance on the WGCNA methodology.
- Borja Valverde Pérez: Conceptualization and main supervisor of the project.
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