Lesson 1 Essential Tools and Basic Requirements

1.1 Microbiome Data Analysis (CDI)

R-first | QIIME2-first | Reproducible workflows

Before analyzing any microbiome data, we establish a reproducible, analysis-ready environment. Environment setup is part of scientific rigor in microbiome research.

1.2 Why basic requirements matter

Microbiome analysis is sensitive to:

software versions
file structure
hidden preprocessing steps

Small inconsistencies can invalidate biological conclusions.

1.3 R environment check

This guide is R-first. We start by confirming the R session and loading core packages.

1.4 Core packages (introduced gradually)

We do not load all packages at once. For now, we only load tidy data tools.

library(tidyverse)

1.5 Project structure

A typical CDI microbiome project uses the following structure:

microbiome-project/
├─ figures/

1.6 Role of QIIME2 in this guide

QIIME2 produces analysis-ready artifacts
Statistical analysis happens in R, not inside QIIME2
ASVs are the default unit of analysis

1.7 Lesson 01 checkpoint

You should now understand:

why environment setup matters
why R is the primary language
how QIIME2 fits into the workflow

Continue to Lesson 02 — Microbiome Data and Metadata Fundamentals