microbiome-analysis 开源项目推荐（208 个）

microbiome /microbiome

microbiome R package

opencobra /cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

YuLab-SMU /MicrobiotaProcess

🦠 A comprehensive R package for deep mining microbiome

qiita-spots /qiita

Qiita - A multi-omics databasing effort

grimmlab /MicrobiomeBestPracticeReview

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

david-barnett /microViz

R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.

microsud /Tools-Microbiome-Analysis

A list of R environment based tools for microbiome data exploration, statistical analysis and visualization

zoecastillo /microbiomeExplorer

The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or through a Shiny application. Written by Janina Reeder and Joseph N. Paulson.

cafferychen777 /MicrobiomeStat

追踪、分析、可视化：用MicrobiomeStat揭开你的微生物组的时间模式

Russel88 /MicEco

Various functions for analysis of microbial community data

waldronlab /curatedMetagenomicDataAnalyses

Analyses in R and Python Using curatedMetagenomicData

wijerasa /bioinformatics-projects

A Collection of Bioinformatics Projects

GPZ-Bioinfo /tmap

topological data analysis of population-scale microbiomes

microsud /microbiomeutilities

The is mostly a wrapper tool using phyloseq and microbiome R packages.

vallenderlab /MicrobiomeR

A comprehensive and customizable R package for microbiome analysis.

mikemc /metacal

Metagenomics calibration R package

CMU-SAFARI /Genome-on-Diet

Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).

guokai8 /microbial

Do microbiome analysis with dada2 and phyloseq object

statdivlab /paramedic

Predicting Absolute and Relative Abundance by Modeling Efficiency to Derive Intervals and Concentrations

smdabdoub /phylotoast

Tools for phylogenetic data analysis including visualization and cluster-computing support.