Statistical Analysis Of Microbiome Data
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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.
Statistical Data Analysis Of Microbiomes And Metabolomics
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Author : Yinglin Xia
language : en
Publisher: American Chemical Society
Release Date : 2022-02-03
Statistical Data Analysis Of Microbiomes And Metabolomics written by Yinglin Xia and has been published by American Chemical Society this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-02-03 with Science categories.
Compared with other research fields, both microbiome and metabolomics data are complicated and have some unique characteristics, respectively. Thus, choosing an appropriate statistical test or method is a very important step in the analysis of microbiome and metabolomics data. However, this is still a difficult task for those biomedical researchers without a statistical background and for those biostatisticians who do not have research experiences in these fields. Graduate students studying microbiome and metabolomics; statisticians, working on microbiome and metabolomics projects, either for their own research, or for their collaborative research for experimental design, grant application, and data analysis; and researchers who investigate biomedical and biochemical projects with the microbiome, metabolome, and multi-omics data analysis will benefit from reading this work.
An Integrated Analysis Of Microbiomes And Metabolomics
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Author : Yinglin Xia
language : en
Publisher: American Chemical Society
Release Date : 2022-03-25
An Integrated Analysis Of Microbiomes And Metabolomics written by Yinglin Xia and has been published by American Chemical Society this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-03-25 with Science categories.
Because the microbial community is dynamic, an individual’s microbiota at a given time is varied, and many factors, including age, host genetics, diet, and the local environment, significantly change the microbiota. Thus, microbiome researchers have naturally expanded their research to look for insights into the interaction of the microbiome with other “omics”. Metabolites (small molecules) are the intermediate or end products of metabolism. Metabolites have various functions. The microbial-derived metabolites play an important role in the function of the microbiome. Thus, the advancement in microbiome studies is becoming particularly critical for the integration of microbial DNA sequencing data with other omics data, especially microbiome-metabolomics integration.
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.
Novel Approaches In Microbiome Analyses And Data Visualization
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Author : Jessica Galloway-Peña
language : en
Publisher: Frontiers Media SA
Release Date : 2019-02-06
Novel Approaches In Microbiome Analyses And Data Visualization written by Jessica Galloway-Peña 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 2019-02-06 with categories.
High-throughput sequencing technologies are widely used to study microbial ecology across species and habitats in order to understand the impacts of microbial communities on host health, metabolism, and the environment. Due to the dynamic nature of microbial communities, longitudinal microbiome analyses play an essential role in these types of investigations. Key questions in microbiome studies aim at identifying specific microbial taxa, enterotypes, genes, or metabolites associated with specific outcomes, as well as potential factors that influence microbial communities. However, the characteristics of microbiome data, such as sparsity and skewedness, combined with the nature of data collection, reflected often as uneven sampling or missing data, make commonly employed statistical approaches to handle repeated measures in longitudinal studies inadequate. Therefore, many researchers have begun to investigate methods that could improve incorporating these features when studying clinical, host, metabolic, or environmental associations with longitudinal microbiome data. In addition to the inferential aspect, it is also becoming apparent that visualization of high dimensional data in a way which is both intelligible and comprehensive is another difficult challenge that microbiome researchers face. Visualization is crucial in both the analysis and understanding of metagenomic data. Researchers must create clear graphic representations that give biological insight without being overly complicated. Thus, this Research Topic seeks to both review and provide novels approaches that are being developed to integrate microbiome data and complex metadata into meaningful mathematical, statistical and computational models. We believe this topic is fundamental to understanding the importance of microbial communities and provides a useful reference for other investigators approaching the field.
Handbook Of Statistical Genomics
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Author : David J. Balding
language : en
Publisher: John Wiley & Sons
Release Date : 2019-07-09
Handbook Of Statistical Genomics written by David J. Balding and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-07-09 with Science categories.
A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.
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.
Microbiome Analysis
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Author : Robert G. Beiko
language : en
Publisher: Humana
Release Date : 2019-10-23
Microbiome Analysis written by Robert G. Beiko and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-10-23 with Science categories.
This volume aims to capture the entire microbiome analysis pipeline, sample collection, quality assurance, and computational analysis of the resulting data. Chapters detail several example applications of microbiome research, and the protocols described in this book are complemented with short perspectives about the history, current state, and future directions of protocols in microbiomics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Microbiome Analysis: Methods and Protocols aims to ensure successful results in the further study of this vital field.