Bioinformatic And Statistical Analysis Of Microbiome Data

Author : Yinglin Xia,Jun Sun
Publisher : Springer Nature
Page : 717 pages
File Size : 51,7 Mb
Release : 2023-06-16
Category : Science
ISBN : 9783031213915

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Bioinformatic and Statistical Analysis of Microbiome Data by Yinglin Xia,Jun Sun Pdf

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.

Author : Somnath Datta,Subharup Guha
Publisher : Springer Nature
Page : 349 pages
File Size : 50,6 Mb
Release : 2021-10-27
Category : Medical
ISBN : 9783030733513

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Statistical Analysis of Microbiome Data by Somnath Datta,Subharup Guha Pdf

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.

Author : Yinglin Xia,Jun Sun,Ding-Geng Chen
Publisher : Springer
Page : 505 pages
File Size : 49,9 Mb
Release : 2018-10-06
Category : Computers
ISBN : 9789811315343

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Statistical Analysis of Microbiome Data with R by Yinglin Xia,Jun Sun,Ding-Geng Chen Pdf

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.

Author : Joao Carlos Setubal,Jens Stoye,Bas E. Dutilh
Publisher : Frontiers Media SA
Page : 170 pages
File Size : 43,7 Mb
Release : 2021-02-02
Category : Science
ISBN : 9782889664375

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Computational Methods for Microbiome Analysis by Joao Carlos Setubal,Jens Stoye,Bas E. Dutilh Pdf

Author : Yinglin Xia,Jun Sun
Publisher : CRC Press
Page : 457 pages
File Size : 53,8 Mb
Release : 2024-07-22
Category : Mathematics
ISBN : 9781040045664

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Applied Microbiome Statistics by Yinglin Xia,Jun Sun Pdf

This unique book officially defines microbiome statistics as a specific new field of statistics and addresses the statistical analysis of correlation, association, interaction, and composition in microbiome research. It also defines the study of the microbiome as a hypothesis-driven experimental science and describes two microbiome research themes and six unique characteristics of microbiome data, as well as investigating challenges for statistical analysis of microbiome data using the standard statistical methods. This book is useful for researchers of biostatistics, ecology, and data analysts. Presents a thorough overview of statistical methods in microbiome statistics of parametric and nonparametric correlation, association, interaction, and composition adopted from classical statistics and ecology and specifically designed for microbiome research. Performs step-by-step statistical analysis of correlation, association, interaction, and composition in microbiome data. Discusses the issues of statistical analysis of microbiome data: high dimensionality, compositionality, sparsity, overdispersion, zero-inflation, and heterogeneity. Investigates statistical methods on multiple comparisons and multiple hypothesis testing and applications to microbiome data. Introduces a series of exploratory tools to visualize composition and correlation of microbial taxa by barplot, heatmap, and correlation plot. Employs the Kruskal–Wallis rank-sum test to perform model selection for further multi-omics data integration. Offers R code and the datasets from the authors’ real microbiome research and publicly available data for the analysis used. Remarks on the advantages and disadvantages of each of the methods used.

Author : Brooke Fridley,Xuefeng Wang
Publisher : Springer Nature
Page : 377 pages
File Size : 49,9 Mb
Release : 2023-03-16
Category : Science
ISBN : 9781071629864

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Statistical Genomics by Brooke Fridley,Xuefeng Wang Pdf

This volume provides a collection of protocols from researchers in the statistical genomics field. Chapters focus on integrating genomics with other “omics” data, such as transcriptomics, epigenomics, proteomics, metabolomics, and metagenomics. 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. Cutting-edge and thorough, Statistical Genomics hopes that by covering these diverse and timely topics researchers are provided insights into future directions and priorities of pan-omics and the precision medicine era.

Author : Xing Chen,Hongsheng Liu,Qi Zhao
Publisher : Frontiers Media SA
Page : 423 pages
File Size : 47,9 Mb
Release : 2020-06-22
Category : Electronic
ISBN : 9782889635634

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Bioinformatics in Microbiota by Xing Chen,Hongsheng Liu,Qi Zhao Pdf

Author : Jessica Galloway-Peña,Michele Guindani
Publisher : Frontiers Media SA
Page : 186 pages
File Size : 40,6 Mb
Release : 2019-02-06
Category : Electronic
ISBN : 9782889456536

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Novel Approaches in Microbiome Analyses and Data Visualization by Jessica Galloway-Peña,Michele Guindani Pdf

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.

Author : Csaba Ortutay,Zsuzsanna Ortutay
Publisher : John Wiley & Sons
Page : 354 pages
File Size : 48,6 Mb
Release : 2017-02-06
Category : Medical
ISBN : 9781119165026

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Molecular Data Analysis Using R by Csaba Ortutay,Zsuzsanna Ortutay Pdf

This book addresses the difficulties experienced by wet lab researchers with the statistical analysis of molecular biology related data. The authors explain how to use R and Bioconductor for the analysis of experimental data in the field of molecular biology. The content is based upon two university courses for bioinformatics and experimental biology students (Biological Data Analysis with R and High-throughput Data Analysis with R). The material is divided into chapters based upon the experimental methods used in the laboratories. Key features include: • Broad appeal--the authors target their material to researchers in several levels, ensuring that the basics are always covered. • First book to explain how to use R and Bioconductor for the analysis of several types of experimental data in the field of molecular biology. • Focuses on R and Bioconductor, which are widely used for data analysis. One great benefit of R and Bioconductor is that there is a vast user community and very active discussion in place, in addition to the practice of sharing codes. Further, R is the platform for implementing new analysis approaches, therefore novel methods are available early for R users.

Author : Naiara Rodríguez-Ezpeleta,Michael Hackenberg,Ana M. Aransay
Publisher : Springer Science & Business Media
Page : 258 pages
File Size : 52,7 Mb
Release : 2011-10-26
Category : Science
ISBN : 9781461407829

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Bioinformatics for High Throughput Sequencing by Naiara Rodríguez-Ezpeleta,Michael Hackenberg,Ana M. Aransay Pdf

Next generation sequencing is revolutionizing molecular biology. Owing to this new technology it is now possible to carry out a panoply of experiments at an unprecedented low cost and high speed. These go from sequencing whole genomes, transcriptomes and small non-coding RNAs to description of methylated regions, identification protein – DNA interaction sites and detection of structural variation. The generation of gigabases of sequence information for each of this huge bandwidth of applications in just a few days makes the development of bioinformatics applications for next generation sequencing data analysis as urgent as challenging.

Author : Warren J. Ewens,Gregory R. Grant
Publisher : Springer Science & Business Media
Page : 485 pages
File Size : 55,6 Mb
Release : 2013-03-09
Category : Medical
ISBN : 9781475732474

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Statistical Methods in Bioinformatics by Warren J. Ewens,Gregory R. Grant Pdf

There was a real need for a book that introduces statistics and probability as they apply to bioinformatics. This book presents an accessible introduction to elementary probability and statistics and describes the main statistical applications in the field.

Author : Robert G. Beiko,Will Hsiao,John Parkinson
Publisher : Unknown
Page : 324 pages
File Size : 48,7 Mb
Release : 2018
Category : Microbiology
ISBN : 1493987283

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Microbiome Analysis by Robert G. Beiko,Will Hsiao,John Parkinson Pdf

Author : Anonim
Publisher : Unknown
Page : 128 pages
File Size : 44,6 Mb
Release : 2024-06-28
Category : Electronic
ISBN : 9789814469098

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New Developments in Biostatistics and Bioinformatics by Anonim Pdf

Author : Rama Kant Dubey,Vishal Tripathi,Ratna Prabha,Rajan Chaurasia,Dhananjaya Pratap Singh,Ch. Srinivasa Rao,Ali El-Keblawy,Purushothaman Chirakkuzhyil Abhilash
Publisher : Springer
Page : 118 pages
File Size : 42,6 Mb
Release : 2019-05-24
Category : Nature
ISBN : 9783030155162

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Unravelling the Soil Microbiome by Rama Kant Dubey,Vishal Tripathi,Ratna Prabha,Rajan Chaurasia,Dhananjaya Pratap Singh,Ch. Srinivasa Rao,Ali El-Keblawy,Purushothaman Chirakkuzhyil Abhilash Pdf

This book explores the significance of soil microbial diversity to understand its utility in soil functions, ecosystem services, environmental sustainability, and achieving the sustainable development goals. With a focus on agriculture and environment, the book highlights the importance of the microbial world by providing state-of-the-art technologies for examining the structural and functional attributes of soil microbial diversity for applications in healthcare, industrial biotechnology, and bioremediation studies. In seven chapters, the book will act as a primer for students, environmental biotechnologists, microbial ecologists, plant scientists, and agricultural microbiologists. Chapter 1 introduces readers to the soil microbiome, and chapter 2 discusses the below ground microbial world. Chapter 3 addresses various methods for exploring microbial diversity, chapter 4 discusses the genomics methods, chapter 5 provides the metaproteomics and metatranscriptomics approaches and chapter 6 details the bioinformatics tools for soil microbial community analysis, and chapter 7 concludes the text with future perspectives on further soil microbial uses and applications.

Author : Shui Qing Ye
Publisher : CRC Press
Page : 208 pages
File Size : 43,8 Mb
Release : 2016-01-13
Category : Computers
ISBN : 9781040056905

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Big Data Analysis for Bioinformatics and Biomedical Discoveries by Shui Qing Ye Pdf

Demystifies Biomedical and Biological Big Data AnalysesBig Data Analysis for Bioinformatics and Biomedical Discoveries provides a practical guide to the nuts and bolts of Big Data, enabling you to quickly and effectively harness the power of Big Data to make groundbreaking biological discoveries, carry out translational medical research, and implem