TonyX1104/GM_diarrhea-nutrition
Domaine:
healthcareType de record:
dataset
Créateur:
Ton
Hôte:
Microbiome analysis of an Ethiopian child cohort (n = 198), relating the gut microbiome to diarrhea, stunting, and thinness.
# Gut Microbiome Associations with Diarrhea and Malnutrition in Ethiopian Schoolchildren
Microbiome analysis of an Ethiopian child cohort (n = 198), relating the gut
microbiome to diarrhea, stunting, and thinness. All analyses read `ps_bacteria_clean.rds`; the R files write figures and tables under `results/`.
## Code
- `analysis.rmd`:
Meta data summary; alpha and beta diversity; taxa composition; genus-level differential abundance (MaAsLin3); PICRUSt2 pathway differential abundance.
- `network.rmd`:
SparCC co-occurrence networks per outcome group (NetCoMi) ; permutation test comparasions and differential edges
- `mediation.rmd`:
Structural-equation mediation of microbiome (CLR PC1) → diarrhea → malnutrition (BAZ / HAZ)
- `ml_ .ipynb`:
Nested-CV Random Forest classifier for the exposure (diarrhea, thinness, stunting) from microbiome vs demographics vs combined features, with permutation importance and ROC.
- `ml_pipeline_utils.py`:
Shared microbiome transformers (prevalence filter, CLR) imported by the ML notebooks
## Data
- `ps_bacteria_clean.rds`:
Cleaned phyloseq object (ASV counts, taxonomy, sample metadata); master input for the R analyses.
- `otu_table.csv`:
Genus-level abundance table (samples × genera), exported for the ML notebooks.
- `sample_data.csv`:
Per-sample metadata: anthropometry, outcomes, qPCR infection status, and demographics.
- `path_abun_*.tsv`:
PICRUSt2 outputs used for pathway analysis
- `path_abun_unstrat.tsv`:
unstratified pathway abundances (pathways × samples)
- `path_abun_unstrat_descrip.tsv`:
same table with a MetaCyc pathway-description column
- `path_abun_contrib.tsv`:
per-sample taxon contributions to each pathway
## Requirements
- R (`*.rmd`):
Bioconductor: `phyloseq`, `maaslin3`, `limma`
GitHub: `NetCoMi` (`stefpeschel/NetCoMi`).
CRAN: `tidyverse`, `vegan`, `ggplot2`, `ggpubr`, `ggrepel`, `ggVennDiagram`,
`gtsummary`, `DT`, `coin`, `Rfit`, `MicrobiomeStat`, `igraph`, `GephiForR`,
`lavaan`, `patchwork`, `gridExtra`, ` …