alpha-diversity 开源项目推荐（23 个）

vallenderlab /MicrobiomeR

A comprehensive and customizable R package for microbiome analysis.

beantkapoor786 /RAPID

RAPID - R based Amplicon Pipeline for Interactive DADA2 - A unified Shiny application that takes you from raw amplicon data to ASV and taxonomy tables with DADA2, and onward to ecology visualizations, PERMANOVA, and ANCOM-BC2 analyses.

philippmuench /AIH_metagenome

code to reproduce AIH results

ilypopv /The-shadow-of-HIV

🦠Research project in Bioinformatics Institute 2023-2024

metagenopolis /ESKRIM

ESKRIM is a reference-free tool that compares microbial richness in shotgun metagenomic samples by counting k-mers

Microbiome-Diversity-Inspector /Microbiome-Diversity-Inspector

Microbiome Diversity Inspector - A platform for visual analysis of microbiome data.

Brochado-Kith /microbiome_analysis

The following codes are focused on microbiome analysis, alpha, beta and relative abundance differences.

jm0535 /0rdin

Ordin: An open-source cross-platform electron desktop application for community ecology analysis.

shivankurkapoor /microbiome-data-analysis

Microbiome Data Analysis

PopovIILab /BatShotMetaFlow

🦇🧫📊Study on bat gut shotgun metagenomics

jvtarss /ccm-2024

Aires-Teixeira, J. V., & Souza, E. (2025). Use of microbial fuel cell systems in wastewater treatment in connection with bioenergy generation. Desafios - Revista Interdisciplinar da Universidade Federal do Tocantins, 12(1), 1–20. https://doi.org/10.20873/pibic_2024_21014.

BolinWo /mbdiv

Microbiome Diversity Analysis Pipeline — alpha/beta diversity + top-N composition in one command

kmvanden /microbiome_analysis

Code and statistical explanations for commonly used microbiome analyses

JTSALAH /Fish-Diversity-Ecology-Assessment

Take advantage of the adehabitat packages in R to determine ecological community richness: including alpha, beta, and gamma diversity!

gkeimiyake /homogeneiza-o-bi-tica

verificacao da homogeneidade biotica em bioma de restinga de mata atlantica atraves de testes de alfa e beta diversidade para riqueza e abundancia de especies

hoang-minh-tho /Automated-Microbiome-R-Pipeline

Automated and reproducible R pipeline for end-to-end bacterial 16S rRNA amplicon sequencing analysis, including ASV inference, taxonomic assignment, diversity analysis, differential abundance testing, and publication-ready visualization.

Nkiruka-Cynthia /microbiome-project1

Microbial community analysis across environments using R

abarghi /Diversity_Using_Vegetarian_and_Tidyverse

Alpha, beta and gamma diversities are computed and visualized using formulas and using the R package vegetarian.

Ahmed-A-Mohamed /metaGEENOME

metaGEENOME is a 16S rRNA metagenomic analysis tool that encompasses nearly all steps of downstream analysis.

A-atakan0 /mikrobiyom-analizi-uc

Gut microbiome in ulcerative colitis by disease severity from full-length Nanopore 16S rRNA (NanoPlot, Chopper, Emu)