AlphaMicrobiome 0.1.3

Microbiome analysis pipeline and toolkit

AlphaMicrobiome

AlphaMicrobiome is a Python‑based toolkit for microbiome data analysis, designed to deliver efficient analytical solutions. It integrates a variety of microbiome analysis algorithms and supports end‑to‑end analysis workflows, ranging from raw data preprocessing to advanced statistical analysis.

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Features

• End‑to‑end workflows – Support for raw sequencing data (FASTQ, FASTA), OTU/ASV tables, and metadata integration.
• Alpha diversity estimation – Shannon, Simpson, Chao1, ACE, Faith’s PD, and more.
• Beta diversity analysis – UniFrac (weighted/unweighted), Bray‑Curtis, Jaccard.
• Taxonomic composition – Phylum‑to‑genus level summarization with interactive bar plots.
• Statistical comparisons – PERMANOVA, ANOSIM, DESeq2‑like differential abundance, LEfSe wrapper.
• Visualization – PCA, PCoA, NMDS, heatmaps, rarefaction curves.
• Python‑first design – Seamless integration with pandas, scikit‑bio, numpy, and matplotlib.

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Installation

Download and install from GitHub:

git clone https://github.com/zhaoy2020/AlphaMicrobiome.git
cd AlphaMicrobiome
pip install -e .

Install directly from PyPi:

pip install AlphaMicrobiome

Tutorial

Detailed tutorials can be found in the notebooks.

Contributing

We welcome contributions! Please follow these steps:

1. Fork the repository and clone it locally.
2. Create a new branch: git checkout -b feature/your-feature-name.
3. Install development dependencies: pip install -e .[dev].
4. Write tests under tests/ and ensure all tests pass: pytest tests/.
5. Update documentation and examples as needed.
6. Push to your fork and open a Pull Request.