Statistics With R For Microbiome Analysis From Raw Reads To Relative Abundance
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Statistics With R For Microbiome Analysis From Raw Reads To Relative Abundance
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Author : Mohsen Nady
language : en
Publisher:
Release Date : 2023-12
Statistics With R For Microbiome Analysis From Raw Reads To Relative Abundance written by Mohsen Nady and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-12 with categories.
This book covers the necessary analysis steps for dealing with microbiome data. The microbial samples are sequenced into raw reads or fastq files. These raw reads should be quality checked to assure their quality per base or per read. Then, after removing the errors, we can infer their exact amplicon sequence variants (ASVs). After that, we taxonomically classify these sequences to represent the different taxonomy levels of species, genus, family, order, class, and phylum and generate a phylogenetic tree. Finally, the sequence data, the taxonomy table, phylogenetic tree, and sample data are combined in a single phyloseq object for ease of plotting, manipulation, and analysis of the different components of microbiome data. The final phyloseq object can also be cleaned for certain low prevalent sequences. All these steps are explained in R codes using a freely available microbiome data of 360 fecal samples.
Statistical Analysis Of Microbiome Data
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Author : Somnath Datta
language : en
Publisher: Springer Nature
Release Date : 2021-10-27
Statistical Analysis Of Microbiome Data written by Somnath Datta and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-10-27 with Medical categories.
Microbiome research has focused on microorganisms that live within the human body and their effects on health. During the last few years, the quantification of microbiome composition in different environments has been facilitated by the advent of high throughput sequencing technologies. The statistical challenges include computational difficulties due to the high volume of data; normalization and quantification of metabolic abundances, relative taxa and bacterial genes; high-dimensionality; multivariate analysis; the inherently compositional nature of the data; and the proper utilization of complementary phylogenetic information. This has resulted in an explosion of statistical approaches aimed at tackling the unique opportunities and challenges presented by microbiome data. This book provides a comprehensive overview of the state of the art in statistical and informatics technologies for microbiome research. In addition to reviewing demonstrably successful cutting-edge methods, particular emphasis is placed on examples in R that rely on available statistical packages for microbiome data. With its wide-ranging approach, the book benefits not only trained statisticians in academia and industry involved in microbiome research, but also other scientists working in microbiomics and in related fields.
Statistical Analysis Of Microbiome Data With R
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Author : Yinglin Xia
language : en
Publisher: Springer
Release Date : 2018-10-06
Statistical Analysis Of Microbiome Data With R written by Yinglin Xia and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-10-06 with Computers categories.
This unique book addresses the statistical modelling and analysis of microbiome data using cutting-edge R software. It includes real-world data from the authors’ research and from the public domain, and discusses the implementation of R for data analysis step by step. The data and R computer programs are publicly available, allowing readers to replicate the model development and data analysis presented in each chapter, so that these new methods can be readily applied in their own research. The book also discusses recent developments in statistical modelling and data analysis in microbiome research, as well as the latest advances in next-generation sequencing and big data in methodological development and applications. This timely book will greatly benefit all readers involved in microbiome, ecology and microarray data analyses, as well as other fields of research.
Bioinformatic And Statistical Analysis Of Microbiome Data
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Author : Yinglin Xia
language : en
Publisher: Springer Nature
Release Date : 2023-06-16
Bioinformatic And Statistical Analysis Of Microbiome Data written by Yinglin Xia and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-06-16 with Science categories.
This unique book addresses the bioinformatic and statistical modelling and also the analysis of microbiome data using cutting-edge QIIME 2 and R software. It covers core analysis topics in both bioinformatics and statistics, which provides a complete workflow for microbiome data analysis: from raw sequencing reads to community analysis and statistical hypothesis testing. It includes real-world data from the authors’ research and from the public domain, and discusses the implementation of QIIME 2 and R for data analysis step-by-step. The data as well as QIIME 2 and R computer programs are publicly available, allowing readers to replicate the model development and data analysis presented in each chapter so that these new methods can be readily applied in their own research. Bioinformatic and Statistical Analysis of Microbiome Data is an ideal book for advanced graduate students and researchers in the clinical, biomedical, agricultural, and environmental fields, as well as those studying bioinformatics, statistics, and big data analysis.
Animal Social Behaviour And Gut Microbiome
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Author : Lifeng Zhu
language : en
Publisher: Frontiers Media SA
Release Date : 2023-09-06
Animal Social Behaviour And Gut Microbiome written by Lifeng Zhu and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-09-06 with Science categories.
Statistical And Computational Methods For Microbiome Multi Omics Data
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Author : Himel Mallick
language : en
Publisher: Frontiers Media SA
Release Date : 2020-11-19
Statistical And Computational Methods For Microbiome Multi Omics Data written by Himel Mallick and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-11-19 with Science categories.
This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.
Advances In Breeding For Wheat Disease Resistance
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Author : Peter Bulli
language : en
Publisher: Frontiers Media SA
Release Date : 2022-11-03
Advances In Breeding For Wheat Disease Resistance written by Peter Bulli and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-11-03 with Science categories.
The Urogenital Microbiota In Urinary Tract Diseases
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Author : A. Lenore Ackerman
language : en
Publisher: Frontiers Media SA
Release Date : 2023-01-10
The Urogenital Microbiota In Urinary Tract Diseases written by A. Lenore Ackerman and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-01-10 with Science categories.
The Oral Microbiome Is A Key Factor In Oral And Systemic Health
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Author : Florence Carrouel
language : en
Publisher: Frontiers Media SA
Release Date : 2022-03-10
The Oral Microbiome Is A Key Factor In Oral And Systemic Health written by Florence Carrouel and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-03-10 with Science categories.
The Female Reproductive Tract Microbiome Gatekeeper For Sexual And Reproductive Health
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Author : Mariya Ivanova Petrova
language : en
Publisher: Frontiers Media SA
Release Date : 2023-03-21
The Female Reproductive Tract Microbiome Gatekeeper For Sexual And Reproductive Health written by Mariya Ivanova Petrova and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-03-21 with Science categories.
An optimal female reproductive tract (FRT) microbiome represents a cornerstone for successful reproductive and sexual health. Although understanding the link between the microbiota and our health is the focus of a growing number of research programs and research has advanced in the last decade, the FRT microbiome remains relatively poorly defined. This is despite it being one of the most critical factors impacting fertility and the health of the future generation. Important gaps in our knowledge remain about women-specific microbial niches, such as the lower FRT. The vaginal microbiome of healthy women is almost exclusively dominated by Lactobacillus species, making these species synonymous with vaginal health. Largely thanks to their capacity to produce high levels of lactic acid, lactobacilli are thought to inhibit most invading bacterial and viral pathogens. Nonetheless, the dogma that all Lactobacillus species are key beneficial species in the vaginal niche has been questioned, based on the association with disease for some of the major players in the niche, for example L. iners, particularly in non-European or Caucasian cohorts. Further, the ability of other (mostly anaerobic) species besides lactobacilli, to maintain similar homeostasis in the vaginal niche raises the question of what we define as optimal or healthy vaginal microbiota. Answering this question is essential since a non-optimal or dysbiotic vaginal microbiome has been linked to the acquisition of sexually transmitted infections (STIs), infertility, and adverse pregnancy outcomes. To confront these healthcare challenges we should be able to distinguish between an optimal and non-optimal microbiome. With the advance of sequence-based technologies, as well as other omics methodologies, including metaproteomics, metabolomics and culturomics, we are now able to begin to correlate the presence, as well as the activities, of specific organisms and microbial communities with health or disease. However, we are only beginning to understand the complexity of interactions between bacterial community members with each other and the human host. A better understanding of these relationships within this specialized environmental niche and in relation to female sexual and reproductive health is critical for the development of novel diagnostics and therapeutics to create and maintain an optimal FRT microbiome.