Population Genetics With R

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Population Genetics With R

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Author : Áki Jarl Láruson
language : en
Publisher: Oxford University Press, USA
Release Date : 2021-02-25

Population Genetics With R written by Áki Jarl Láruson and has been published by Oxford University Press, USA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-02-25 with Computers categories.

This book focuses on applying the hugely popular R software specifically to the field, offering an accessible, step-by-step guide to tackling the challenges of achieving effective data interpretation and summary.

Population Genetics With R

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Author : Áki Jarl Láruson
language : en
Publisher: Oxford University Press
Release Date : 2021-02-24

Population Genetics With R written by Áki Jarl Láruson and has been published by Oxford University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-02-24 with Science categories.

Population genetics is an inherently quantitative discipline, yet often focuses upon abstract concepts which can be difficult to conceptualize and appropriately visualize at first glance. This book focuses on applying the hugely popular R software specifically to the field, offering an accessible, step-by-step guide to tackling the challenges of achieving effective data interpretation and summary. The authors adopt an engaging "learning by doing" approach that will enable readers to develop an intuitive understanding of key population genetics concepts through the use of R. Beginning with the groundwork of installing and using R (including CRAN and the RStudio IDE), the book works through the use of basic commands for data manipulation. An introduction to basic terminology in population genetics follows, clearly explaining how these fundamental assumptions can provide insights and form basic inferences for real populations. The focus then moves onto statistical tests including writing and running algorithms as functions. Subsequent chapters examine genetic variation, adaptation, and natural selection as well as different approaches to population differences. Importantly, the accompanying set of practical exercises demonstrate that implementing all of these concepts via programming can actually help greatly in understanding them, even if they may at first seem insurmountably complex. Finally, this accessible textbook points the way forwards to other key concepts that are important to understanding modern day population genetics research (in particular coalescent theory) and offers the reader useful launching points for further learning. Population Genetics with R is aimed at students ranging from undergraduate to postgraduate level in the fields of population genetics, ecology, evolutionary biology, conservation genetics, computational biology, and biostatistics.

Applied Statistical Genetics With R

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Author : Andrea S. Foulkes
language : en
Publisher: Springer Science & Business Media
Release Date : 2009-04-28

Applied Statistical Genetics With R written by Andrea S. Foulkes and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-04-28 with Science categories.

Statistical genetics has become a core course in many graduate programs in public health and medicine. This book presents fundamental concepts and principles in this emerging field at a level that is accessible to students and researchers with a first course in biostatistics. Extensive examples are provided using publicly available data and the open source, statistical computing environment, R.

Population Genomics With R

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Author : Emmanuel Paradis
language : en
Publisher: CRC Press
Release Date : 2020-05-05

Population Genomics With R written by Emmanuel Paradis and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-05-05 with Mathematics categories.

Population Genomics With R presents a multidisciplinary approach to the analysis of population genomics. The methods treated cover a large number of topics from traditional population genetics to large-scale genomics with high-throughput sequencing data. Several dozen R packages are examined and integrated to provide a coherent software environment with a wide range of computational, statistical, and graphical tools. Small examples are used to illustrate the basics and published data are used as case studies. Readers are expected to have a basic knowledge of biology, genetics, and statistical inference methods. Graduate students and post-doctorate researchers will find resources to analyze their population genetic and genomic data as well as help them design new studies. The first four chapters review the basics of population genomics, data acquisition, and the use of R to store and manipulate genomic data. Chapter 5 treats the exploration of genomic data, an important issue when analysing large data sets. The other five chapters cover linkage disequilibrium, population genomic structure, geographical structure, past demographic events, and natural selection. These chapters include supervised and unsupervised methods, admixture analysis, an in-depth treatment of multivariate methods, and advice on how to handle GIS data. The analysis of natural selection, a traditional issue in evolutionary biology, has known a revival with modern population genomic data. All chapters include exercises. Supplemental materials are available on-line (http://ape-package.ird.fr/PGR.html).

Population Genetics And Microevolutionary Theory

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Author : Alan R. Templeton
language : en
Publisher: John Wiley & Sons
Release Date : 2006-09-29

Population Genetics And Microevolutionary Theory written by Alan R. Templeton 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 2006-09-29 with Science categories.

The advances made possible by the development of molecular techniques have in recent years revolutionized quantitative genetics and its relevance for population genetics. Population Genetics and Microevolutionary Theory takes a modern approach to population genetics, incorporating modern molecular biology, species-level evolutionary biology, and a thorough acknowledgment of quantitative genetics as the theoretical basis for population genetics. Logically organized into three main sections on population structure and history, genotype-phenotype interactions, and selection/adaptation Extensive use of real examples to illustrate concepts Written in a clear and accessible manner and devoid of complex mathematical equations Includes the author's introduction to background material as well as a conclusion for a handy overview of the field and its modern applications Each chapter ends with a set of review questions and answers Offers helpful general references and Internet links

Human Population Genetics And Genomics

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Author : Alan R. Templeton
language : en
Publisher: Academic Press
Release Date : 2018-11-08

Human Population Genetics And Genomics written by Alan R. Templeton and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-11-08 with Science categories.

Human Population Genetics and Genomics provides researchers/students with knowledge on population genetics and relevant statistical approaches to help them become more effective users of modern genetic, genomic and statistical tools. In-depth chapters offer thorough discussions of systems of mating, genetic drift, gene flow and subdivided populations, human population history, genotype and phenotype, detecting selection, units and targets of natural selection, adaptation to temporally and spatially variable environments, selection in age-structured populations, and genomics and society. As human genetics and genomics research often employs tools and approaches derived from population genetics, this book helps users understand the basic principles of these tools. In addition, studies often employ statistical approaches and analysis, so an understanding of basic statistical theory is also needed. Comprehensively explains the use of population genetics and genomics in medical applications and research Discusses the relevance of population genetics and genomics to major social issues, including race and the dangers of modern eugenics proposals Provides an overview of how population genetics and genomics helps us understand where we came from as a species and how we evolved into who we are now

Evolutionary Genetics

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Author : Glenn-Peter Sætre
language : en
Publisher: Oxford University Press, USA
Release Date : 2019-05

Evolutionary Genetics written by Glenn-Peter Sætre and has been published by Oxford University Press, USA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-05 with Science categories.

Evolutionary genetics is the study of how genetic variation leads to evolutionary change. With the recent explosion in the availability of whole genome sequence data, vast quantities of genetic data are being generated at an ever-increasing pace with the result that programming has become an essential tool for researchers. Most importantly, a thorough understanding of evolutionary principles is essential for making sense of this genetic data. This up-to-date textbook covers all the major components of modern evolutionary genetics, carefully explaining fundamental processes such as mutation, natural selection, genetic drift, and speciation, together with their consequences. The book also draws on a rich literature of exciting and inspiring examples to demonstrate the diversity of evolutionary research, including an emphasis on how evolution and selection has shaped our own species. Furthermore, at the end of each chapter, study questions are provided to motivate the reader to think and reflect on the concepts introduced. Practical experience is essential when it comes to developing an understanding of how to use genetic and genomic data to analyze and address interesting questions in the life sciences and how to interpret results in meaningful ways. In addition to the main text, a series of online tutorials using the R language serves as an introduction to programming, statistics, and the analysis of evolutionary genetic data. The R environment stands out as an ideal all-purpose, open source platform to handle and analyze such data. The book and its online materials take full advantage of the authors' own experience in working in a post-genomic revolution world, and introduce readers to the plethora of molecular and analytical methods that have only recently become available.

Evolution And Population Genetics

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Author :
language : en
Publisher:
Release Date : 2006

Evolution And Population Genetics written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006 with categories.

Population Genetics For Animal Conservation

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Author : Giorgio Bertorelle
language : en
Publisher: Cambridge University Press
Release Date : 2009-05-28

Population Genetics For Animal Conservation written by Giorgio Bertorelle and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-05-28 with Nature categories.

Illustrates the power and utility of the synergy between population genetics and conservation biology in animal conservation.

Primer To Analysis Of Genomic Data Using R

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Author : Cedric Gondro
language : en
Publisher: Springer
Release Date : 2015-05-18

Primer To Analysis Of Genomic Data Using R written by Cedric Gondro and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-05-18 with Medical categories.

Through this book, researchers and students will learn to use R for analysis of large-scale genomic data and how to create routines to automate analytical steps. The philosophy behind the book is to start with real world raw datasets and perform all the analytical steps needed to reach final results. Though theory plays an important role, this is a practical book for graduate and undergraduate courses in bioinformatics and genomic analysis or for use in lab sessions. How to handle and manage high-throughput genomic data, create automated workflows and speed up analyses in R is also taught. A wide range of R packages useful for working with genomic data are illustrated with practical examples. The key topics covered are association studies, genomic prediction, estimation of population genetic parameters and diversity, gene expression analysis, functional annotation of results using publically available databases and how to work efficiently in R with large genomic datasets. Important principles are demonstrated and illustrated through engaging examples which invite the reader to work with the provided datasets. Some methods that are discussed in this volume include: signatures of selection, population parameters (LD, FST, FIS, etc); use of a genomic relationship matrix for population diversity studies; use of SNP data for parentage testing; snpBLUP and gBLUP for genomic prediction. Step-by-step, all the R code required for a genome-wide association study is shown: starting from raw SNP data, how to build databases to handle and manage the data, quality control and filtering measures, association testing and evaluation of results, through to identification and functional annotation of candidate genes. Similarly, gene expression analyses are shown using microarray and RNAseq data. At a time when genomic data is decidedly big, the skills from this book are critical. In recent years R has become the de facto tool for analysis of gene expression data, in addition to its prominent role in analysis of genomic data. Benefits to using R include the integrated development environment for analysis, flexibility and control of the analytic workflow. Included topics are core components of advanced undergraduate and graduate classes in bioinformatics, genomics and statistical genetics. This book is also designed to be used by students in computer science and statistics who want to learn the practical aspects of genomic analysis without delving into algorithmic details. The datasets used throughout the book may be downloaded from the publisher’s website.