yongxinliu / qiime2chinesemanual

QIIME 2中文文档(QIIME 2 Chinese Manual)

QIIME 2中文文档(QIIME 2 Chinese Manual)

本项目是QIIME 2官网的中文翻译：

• 英文原版每季度更新，目前更新至2023.5
• 中文简明教程，每季度更新一次 https://github.com/YongxinLiu/EasyAmplicon/tree/master/qiime2 ，与英文原版同步
• 中文完整文档，每年更新一次

软件更新较快，如果有问题以英文官网教程为准

英文官网

QIIME 2主页：https://qiime2.org/

QIIME 2英文官网教程：https://docs.qiime2.org/2023.5/

QIIME 2英文开发版：https://github.com/qiime2/docs

中文简明教程

最新代码：https://github.com/YongxinLiu/EasyAmplicon/tree/master/qiime2

• 流程代码：pipeline_qiime2.sh
• 中文简明教程：使用QIIME 2分析微生物组16S rRNA基因扩增子测序数据 https://bio-protocol.org/bio101/e2003554

中文完整文档

持续更新中...

QIIME 2教程中文完整文档(2023.5)

• NBT：QIIME 2可重复、交互式的微生物组分析平台
• 1简介和安装Introduction&Install
• 2插件工作流程概述Workflow
• 3老司机上路指南Experienced
• Genome Biology：人体各部位微生物组时间序列分析
• 4人体各部位微生物组分析Moving Pictures
• 5粪菌移植分析练习FMT
• Microbiome：粪菌移植改善自闭症
• 6沙漠土壤分析Atacama soil
• mSystems：干旱对土壤微生物组的影响
• 7帕金森小鼠教程Parkinson's Mouse
• Cell：肠道菌群促进帕金森发生ParkinsonDisease
• 8差异丰度分析gneiss
• 9数据导入Importing data
• 10数据导出Exporting data
• 11元数据Metadata
• 12数据筛选Filtering data
• 13训练特征分类器Training feature classifiers
• 14数据评估和质控Evaluating and controlling
• 15样品分类和回归q2-sample-classifier
• 16纵向和成对样本比较q2-longitudinal
• 17鉴定和过滤嵌合体序列q2-vsearch
• 18序列双端合并read-joining
• 19使用q2-vsearch聚类OTUs
• 20实用程序Utilities
• 21进化树推断q2-phylogeny
• 22命令行界面q2cli
• 23图形界面q2studio
• 24Python命令行模式Artifact API
• 25可用和开发中插件AvailableFuturePlugins
• 26开发新插件DevelopingPlugin
• 27语义类型Semantic
• 28社区Community
• 29参考数据库DataResources
• 30补充资源SupplementaryResources
• 31名词Glossary
• 32如何写方法和引用Citing

引用

Evan Bolyen, Jai Ram Rideout, Matthew R. Dillon, Nicholas A. Bokulich, Christian C. Abnet, Gabriel A. Al-Ghalith, Harriet Alexander, Eric J. Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E. Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J. Brislawn, C. Titus Brown, Benjamin J. Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily K. Cope, Ricardo Da Silva, Christian Diener, Pieter C. Dorrestein, Gavin M. Douglas, Daniel M. Durall, Claire Duvallet, Christian F. Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M. Gauglitz, Sean M. Gibbons, Deanna L. Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin A. Huttley, Stefan Janssen, Alan K. Jarmusch, Lingjing Jiang, Benjamin D. Kaehler, Kyo Bin Kang, Christopher R. Keefe, Paul Keim, Scott T. Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan G. I. Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D. Martin, Daniel McDonald, Lauren J. McIver, Alexey V. Melnik, Jessica L. Metcalf, Sydney C. Morgan, Jamie T. Morton, Ahmad Turan Naimey, Jose A. Navas-Molina, Louis Felix Nothias, Stephanie B. Orchanian, Talima Pearson, Samuel L. Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S. Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R. Spear, Austin D. Swafford, Luke R. Thompson, Pedro J. Torres, Pauline Trinh, Anupriya Tripathi, Peter J. Turnbaugh, Sabah Ul-Hasan, Justin J. J. van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C. Weber, Charles H. D. Williamson, Amy D. Willis, Zhenjiang Zech Xu, Jesse R. Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight & J. Gregory Caporaso. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37, 852-857, https://doi.org/10.1038/s41587-019-0209-9

中文版维护：刘永鑫，微信: yongxinliu，邮箱：[email protected] Copyright 2016-2023

qiime2chinesemanual's Issues

qiime diversity alpha 计算出的simpson和simpson_e指数的区别

请问从qiime diversity alpha 计算出的simpson和simpson_e指数的区别是什么呢，两者数值大小与多样性的大小的关系是什么呢？

Sorry to bother you, but can you tell me the difference between the simpson and simpson_e indices？
And how the size of the number relates to the size of the diversity