Population Genomics With R

Download Population Genomics With R full books in PDF, epub, and Kindle. Read online Population Genomics With R ebook anywhere anytime directly on your device. Fast Download speed and no annoying ads. We cannot guarantee that every ebooks is available!

Population Genomics with R

Author : Emmanuel Paradis
Publisher : CRC Press
ISBN 13 : 0429882424
Total Pages : 326 pages
Book Rating : 4.4/5 (298 download)

DOWNLOAD NOW!

Book Synopsis Population Genomics with R by : Emmanuel Paradis

Download or read book Population Genomics with R written by Emmanuel Paradis and published by CRC Press. This book was released on 2020-03-13 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 Genomics

Author : Om P. Rajora
Publisher : Springer
ISBN 13 : 3030045897
Total Pages : 824 pages
Book Rating : 4.0/5 (3 download)

DOWNLOAD NOW!

Book Synopsis Population Genomics by : Om P. Rajora

Download or read book Population Genomics written by Om P. Rajora and published by Springer. This book was released on 2019-01-07 with total page 824 pages. Available in PDF, EPUB and Kindle. Book excerpt: Population genomics has revolutionized various disciplines of biology including population, evolutionary, ecological and conservation genetics, plant and animal breeding, human health, medicine and pharmacology by allowing to address novel and long-standing questions with unprecedented power and accuracy. It employs large-scale or genome-wide genetic information and bioinformatics to address various fundamental and applied aspects in biology and related disciplines, and provides a comprehensive genome-wide perspective and new insights that were not possible before. These advances have become possible due to the development of new and low-cost sequencing and genotyping technologies and novel statistical approaches and software, bioinformatics tools, and models. Population genomics is tremendously advancing our understanding the roles of evolutionary processes, such as mutation, genetic drift, gene flow, and natural selection, in shaping up genetic variation at individual loci and across the genome and populations; improving the assessment of population genetic parameters or processes such as adaptive evolution, effective population size, gene flow, admixture, inbreeding and outbreeding depression, demography, and biogeography; resolving evolutionary histories and phylogenetic relationships of extant, ancient and extinct species; understanding the genomic basis of fitness, adaptation, speciation, complex ecological and economically important traits, and disease and insect resistance; facilitating forensics, genetic medicine and pharmacology; delineating conservation genetic units; and understanding the genetic effects of resource management practices, and assisting conservation and sustainable management of genetic resources. This Population Genomics book discusses the concepts, approaches, applications and promises of population genomics in addressing most of the above fundamental and applied crucial aspects in a variety of organisms from microorganisms to humans. The book provides insights into a range of emerging population genomics topics including population epigenomics, landscape genomics, seascape genomics, paleogenomics, ecological and evolutionary genomics, biogeography, demography, speciation, admixture, colonization and invasion, genomic selection, and plant and animal domestication. This book fills a vacuum in the field and is expected to become a primary reference in Population Genomics world-wide.

Population Genomics: Marine Organisms

Author : Marjorie F. Oleksiak
Publisher : Springer Nature
ISBN 13 : 3030379361
Total Pages : 458 pages
Book Rating : 4.0/5 (33 download)

DOWNLOAD NOW!

Book Synopsis Population Genomics: Marine Organisms by : Marjorie F. Oleksiak

Download or read book Population Genomics: Marine Organisms written by Marjorie F. Oleksiak and published by Springer Nature. This book was released on 2019-12-31 with total page 458 pages. Available in PDF, EPUB and Kindle. Book excerpt: Population genomics has provided unprecedented opportunities to unravel the mysteries of marine organisms in the oceans' depths. The world's oceans, which make up 70% of our planet, encompass diverse habitats and host numerous unexplored populations and species. Population genomics studies of marine organisms are rapidly emerging and have the potential to transform our understanding of marine populations, species, and ecosystems, providing insights into how these organisms are evolving and how they respond to different stimuli and environments. This knowledge is critical for understanding the fundamental aspects of marine life, how marine organisms will respond to environmental changes, and how we can better protect and preserve marine biodiversity and resources. This book brings together leading experts in the field to address critical aspects of fundamental and applied research in marine species and share their research and insights crucial for understanding marine ecosystem diversity and function. It also discusses the challenges, opportunities and future perspectives of marine population genomics.

Applied Statistical Genetics with R

Author : Andrea S. Foulkes
Publisher : Springer Science & Business Media
ISBN 13 : 038789554X
Total Pages : 264 pages
Book Rating : 4.3/5 (878 download)

DOWNLOAD NOW!

Book Synopsis Applied Statistical Genetics with R by : Andrea S. Foulkes

Download or read book Applied Statistical Genetics with R written by Andrea S. Foulkes and published by Springer Science & Business Media. This book was released on 2009-04-28 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 Genetics and Microevolutionary Theory

Author : Alan R. Templeton
Publisher : John Wiley & Sons
ISBN 13 : 0470047216
Total Pages : 720 pages
Book Rating : 4.4/5 (7 download)

DOWNLOAD NOW!

Book Synopsis Population Genetics and Microevolutionary Theory by : Alan R. Templeton

Download or read book Population Genetics and Microevolutionary Theory written by Alan R. Templeton and published by John Wiley & Sons. This book was released on 2006-09-29 with total page 720 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Population Genomics: Wildlife

Author : Paul A. Hohenlohe
Publisher : Springer Nature
ISBN 13 : 3030634892
Total Pages : 559 pages
Book Rating : 4.0/5 (36 download)

DOWNLOAD NOW!

Book Synopsis Population Genomics: Wildlife by : Paul A. Hohenlohe

Download or read book Population Genomics: Wildlife written by Paul A. Hohenlohe and published by Springer Nature. This book was released on 2020-12-09 with total page 559 pages. Available in PDF, EPUB and Kindle. Book excerpt: Population genomics is revolutionizing wildlife biology, conservation, and management by providing key and novel insights into genetic, population and landscape-level processes in wildlife, with unprecedented power and accuracy. This pioneering book presents the advances and potential of population genomics in wildlife, outlining key population genomics concepts and questions in wildlife biology, population genomics approaches that are specifically applicable to wildlife, and application of population genomics in wildlife population and evolutionary biology, ecology, adaptation and conservation and management. It is important for students, researchers, and wildlife professionals to understand the growing set of population genomics tools that can address issues from delineation of wildlife populations to assessing their capacity to adapt to environmental change. This book brings together leading experts in wildlife population genomics to discuss the key areas of the field, as well as challenges, opportunities and future prospects of wildlife population genomics.

Human Population Genetics and Genomics

Author : Alan R. Templeton
Publisher : Academic Press
ISBN 13 : 0123860261
Total Pages : 500 pages
Book Rating : 4.1/5 (238 download)

DOWNLOAD NOW!

Book Synopsis Human Population Genetics and Genomics by : Alan R. Templeton

Download or read book Human Population Genetics and Genomics written by Alan R. Templeton and published by Academic Press. This book was released on 2018-11-08 with total page 500 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Introduction to Genomics

Author : Arthur Lesk
Publisher : Oxford University Press, USA
ISBN 13 : 0199564353
Total Pages : 421 pages
Book Rating : 4.1/5 (995 download)

DOWNLOAD NOW!

Book Synopsis Introduction to Genomics by : Arthur Lesk

Download or read book Introduction to Genomics written by Arthur Lesk and published by Oxford University Press, USA. This book was released on 2012 with total page 421 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers the latest techniques that enable us to study the genome in detail, the book explores what the genome tells us about life at the level of the molecule, the cell, and the organism

Statistical Population Genomics

Author : Julien Y Dutheil
Publisher :
ISBN 13 : 9781013271403
Total Pages : 464 pages
Book Rating : 4.2/5 (714 download)

DOWNLOAD NOW!

Book Synopsis Statistical Population Genomics by : Julien Y Dutheil

Download or read book Statistical Population Genomics written by Julien Y Dutheil and published by . This book was released on 2020-10-08 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access volume presents state-of-the-art inference methods in population genomics, focusing on data analysis based on rigorous statistical techniques. After introducing general concepts related to the biology of genomes and their evolution, the book covers state-of-the-art methods for the analysis of genomes in populations, including demography inference, population structure analysis and detection of selection, using both model-based inference and simulation procedures. Last but not least, it offers an overview of the current knowledge acquired by applying such methods to a large variety of eukaryotic organisms. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, pointers to the relevant literature, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Statistical Population Genomics aims to promote and ensure successful applications of population genomic methods to an increasing number of model systems and biological questions. This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors.

Conservation and the Genomics of Populations

Author : Fred W. Allendorf
Publisher : Oxford University Press
ISBN 13 : 0198856563
Total Pages : 785 pages
Book Rating : 4.1/5 (988 download)

DOWNLOAD NOW!

Book Synopsis Conservation and the Genomics of Populations by : Fred W. Allendorf

Download or read book Conservation and the Genomics of Populations written by Fred W. Allendorf and published by Oxford University Press. This book was released on 2022 with total page 785 pages. Available in PDF, EPUB and Kindle. Book excerpt: The relentless loss of biodiversity is among the greatest problems facing the world today. The third edition of this established textbook provides an updated and comprehensive overview of the essential background, concepts, and tools required to understand how genetics can be used to conservespecies, reduce threat of extinction, and manage species of ecological or commercial importance. This edition is thoroughly revised to reflect the major contribution of genomics to conservation of populations and species. It includes two new chapters: "Genetic Monitoring" and a final "ConservationGenetics in Practice" chapter that addresses the role of science and policy in conservation genetics.New genomic techniques and statistical analyses are crucial tools for the conservation geneticist. This accessible and authoritative textbook provides an essential toolkit grounded in population genetics theory, coupled with basic and applied research examples from plants, animals, and microbes. Thebook examines genetic and phenotypic variation in natural populations, the principles and mechanisms of evolutionary change, evolutionary response to anthropogenic change, and applications in conservation and management.Conservation and the Genomics of Populations helps demystify genetics and genomics for conservation practitioners and early career scientists, so that population genetic theory and new genomic data can help raise the bar in conserving biodiversity in the most critical 20 year period in the historyof life on Earth. It is aimed at a global market of applied population geneticists, conservation practitioners, and natural resource managers working for wildlife and habitat management agencies. It will be of particular relevance and use to upper undergraduate and graduate students taking coursesin conservation biology, conservation genetics, and wildlife management.

The Amaranth Genome

Author : Dinesh Adhikary
Publisher : Springer Nature
ISBN 13 : 3030723658
Total Pages : 181 pages
Book Rating : 4.0/5 (37 download)

DOWNLOAD NOW!

Book Synopsis The Amaranth Genome by : Dinesh Adhikary

Download or read book The Amaranth Genome written by Dinesh Adhikary and published by Springer Nature. This book was released on 2021-06-01 with total page 181 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the development of genetic resources in amaranths, with a major focus on genomics, reverse, and forward genetics tools and strategies that have been developed for crop improvement. Amaranth is an ancient crop native to the New World. Interest in amaranths is being renewed, due to their adaptability, stress tolerance, and nutritional value. There are about 65 species in the genus, including Amaranthus caudatus L., A. cruentus L., and A. hypochondriacus L., which are primarily grown as protein-rich grains or pseudocereals. The genus also includes major noxious weeds (e.g., A. palmeri). The amaranths are within the Caryophyllales order and thus many species (e.g., A. tricolor) produce red (betacyanin) or yellow (betaxanthin) betalain pigments, which are chemically distinct from the anthocyanins responsible for red pigmentation in other plants. A. hypochondriacus, which shows disomic inheritance (2n = 32; n= 466 Mb), has been sequenced and annotated with 23,059 protein-coding genes. Additional members of the genus are now also been sequenced including weedy amaranths, other grain amaranths, and their putative progenitors.

Primer to Analysis of Genomic Data Using R

Author : Cedric Gondro
Publisher : Springer
ISBN 13 : 3319144758
Total Pages : 283 pages
Book Rating : 4.3/5 (191 download)

DOWNLOAD NOW!

Book Synopsis Primer to Analysis of Genomic Data Using R by : Cedric Gondro

Download or read book Primer to Analysis of Genomic Data Using R written by Cedric Gondro and published by Springer. This book was released on 2015-05-18 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Theories of Population Variation in Genes and Genomes

Author : Freddy Bugge Christiansen
Publisher : Princeton University Press
ISBN 13 : 0691165890
Total Pages : 431 pages
Book Rating : 4.6/5 (911 download)

DOWNLOAD NOW!

Book Synopsis Theories of Population Variation in Genes and Genomes by : Freddy Bugge Christiansen

Download or read book Theories of Population Variation in Genes and Genomes written by Freddy Bugge Christiansen and published by Princeton University Press. This book was released on 2014-11-23 with total page 431 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook provides an authoritative introduction to both classical and coalescent approaches to population genetics. Written for graduate students and advanced undergraduates by one of the world's leading authorities in the field, the book focuses on the theoretical background of population genetics, while emphasizing the close interplay between theory and empiricism. Traditional topics such as genetic and phenotypic variation, mutation, migration, and linkage are covered and advanced by contemporary coalescent theory, which describes the genealogy of genes in a population, ultimately connecting them to a single common ancestor. Effects of selection, particularly genomic effects, are discussed with reference to molecular genetic variation. The book is designed for students of population genetics, bioinformatics, evolutionary biology, molecular evolution, and theoretical biology--as well as biologists, molecular biologists, breeders, biomathematicians, and biostatisticians. Contains up-to-date treatment of key areas in classical and modern theoretical population genetics Provides in-depth coverage of coalescent theory Discusses genomic effects of selection Gives examples from empirical population genetics Incorporates figures, diagrams, and boxed features throughout Includes end-of-chapter exercises Speaks to a wide range of students in biology, bioinformatics, and biostatistics

Handbook of Statistical Genomics

Author : David J. Balding
Publisher : John Wiley & Sons
ISBN 13 : 1119429250
Total Pages : 1740 pages
Book Rating : 4.1/5 (194 download)

DOWNLOAD NOW!

Book Synopsis Handbook of Statistical Genomics by : David J. Balding

Download or read book Handbook of Statistical Genomics written by David J. Balding and published by John Wiley & Sons. This book was released on 2019-07-09 with total page 1740 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Paleogenomics

Author : Charlotte Lindqvist
Publisher : Springer
ISBN 13 : 3030047539
Total Pages : 432 pages
Book Rating : 4.0/5 (3 download)

DOWNLOAD NOW!

Book Synopsis Paleogenomics by : Charlotte Lindqvist

Download or read book Paleogenomics written by Charlotte Lindqvist and published by Springer. This book was released on 2019-01-07 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in genome-scale DNA sequencing technologies have revolutionized genetic research on ancient organisms, extinct species, and past environments. When it is recoverable after hundreds or thousands of years of unintended preservation, “ancient DNA” (or aDNA) is often highly degraded, necessitating specialized handling and analytical approaches. Paleogenomics defines the field of reconstructing and analyzing the genomes of historic or long-dead organisms, most often through comparison with modern representatives of the same or similar species. The opportunity to isolate and study paleogenomes has radically transformed many fields, spanning biology, anthropology, agriculture, and medicine. Examples include understanding evolutionary relationships of extinct species known only from fossils, the domestication of plants and animals, and the evolution and geographical spread of certain pathogens. This pioneering book presents a snapshot view of the history, current status, and future prospects of paleogenomics, taking a broad viewpoint that covers a range of topics and organisms to provide an up-to-date status of the applications, challenges, and promise of the field. This book is intended for a variety of readerships, including upper-level undergraduate and graduate students, professionals and experts in the field, as well as anyone excited by the extraordinary insights that paleogenomics offers.

Evaluating Human Genetic Diversity

Author : National Research Council
Publisher : National Academies Press
ISBN 13 : 0309184746
Total Pages : 101 pages
Book Rating : 4.3/5 (91 download)

DOWNLOAD NOW!

Book Synopsis Evaluating Human Genetic Diversity by : National Research Council

Download or read book Evaluating Human Genetic Diversity written by National Research Council and published by National Academies Press. This book was released on 1998-01-19 with total page 101 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book assesses the scientific value and merit of research on human genetic differencesâ€"including a collection of DNA samples that represents the whole of human genetic diversityâ€"and the ethical, organizational, and policy issues surrounding such research. Evaluating Human Genetic Diversity discusses the potential uses of such collection, such as providing insight into human evolution and origins and serving as a springboard for important medical research. It also addresses issues of confidentiality and individual privacy for participants in genetic diversity research studies.

Molecular Population Genetics

Author : Matthew William Hahn
Publisher : Sinauer Associates, Incorporated
ISBN 13 : 9780878939657
Total Pages : 334 pages
Book Rating : 4.9/5 (396 download)

DOWNLOAD NOW!

Book Synopsis Molecular Population Genetics by : Matthew William Hahn

Download or read book Molecular Population Genetics written by Matthew William Hahn and published by Sinauer Associates, Incorporated. This book was released on 2018 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: Published by Sinauer Associates, an imprint of Oxford University Press. Provides descriptions of the methods and tools used in molecular population genetics, which has combined advances in molecular biology and genomics with mathematical and empirical findings to uncover the history of natural selection and demographic shifts in many organisms.