Metagenomics Data Visualization and Analysis in R

I am a PhD researcher (wet-lab focus) working on the neonatal microbiome. I have Illumina shotgun metagenomics datasets that I already processed using CZID (formerly IDseq). I now want to perform further data analysis and visualization in R.

What I need help with

Importing and structuring CZID output into R (phyloseq or similar format)

Generating high-quality figures:

Taxonomic composition (stacked bar plots)

Heatmaps of abundant taxa

Ordination plots (PCoA, NMDS with Bray–Curtis)

Alpha diversity (Shannon, Simpson, etc.)


Guidance on best practices for low-biomass/neonatal samples (contaminant handling, normalization)

(Optional) Basic statistical testing (differential abundance, group comparisons)

Delivering clean, reproducible R scripts so I can re-run and learn from them


What I provide

Processed CZID taxonomic tables (CSV format)

Metadata sheet with sample IDs and variables (e.g., group, timepoint)

Specific questions about plots/analyses


Who I’m looking for

Experience in microbiome / metagenomics data analysis

Strong R/phyloseq skills (visualization and statistics)

Ability to explain workflow steps clearly to a wet-lab researcher

Bonus: familiarity with neonatal or low-biomass microbiome datasets


Deliverables

A set of publication-ready figures (PNG/PDF)

Annotated R scripts for reproducibility and self-learning

Short online consultation / Q&A session


If you are interested, please share:

Examples of similar microbiome plots/analyses you’ve done

Your typical turnaround time

Your rate (hourly or fixed-price)