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Applied Statistical Genetics with R by Andrea S. Foulkes Pdf
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.
An Introduction to Statistical Genetic Data Analysis by Melinda C. Mills,Nicola Barban,Felix C. Tropf Pdf
A comprehensive introduction to modern applied statistical genetic data analysis, accessible to those without a background in molecular biology or genetics. Human genetic research is now relevant beyond biology, epidemiology, and the medical sciences, with applications in such fields as psychology, psychiatry, statistics, demography, sociology, and economics. With advances in computing power, the availability of data, and new techniques, it is now possible to integrate large-scale molecular genetic information into research across a broad range of topics. This book offers the first comprehensive introduction to modern applied statistical genetic data analysis that covers theory, data preparation, and analysis of molecular genetic data, with hands-on computer exercises. It is accessible to students and researchers in any empirically oriented medical, biological, or social science discipline; a background in molecular biology or genetics is not required. The book first provides foundations for statistical genetic data analysis, including a survey of fundamental concepts, primers on statistics and human evolution, and an introduction to polygenic scores. It then covers the practicalities of working with genetic data, discussing such topics as analytical challenges and data management. Finally, the book presents applications and advanced topics, including polygenic score and gene-environment interaction applications, Mendelian Randomization and instrumental variables, and ethical issues. The software and data used in the book are freely available and can be found on the book's website.
Statistics and Data with R by Yosef Cohen,Jeremiah Y. Cohen Pdf
R, an Open Source software, has become the de facto statistical computing environment. It has an excellent collection of data manipulation and graphics capabilities. It is extensible and comes with a large number of packages that allow statistical analysis at all levels – from simple to advanced – and in numerous fields including Medicine, Genetics, Biology, Environmental Sciences, Geology, Social Sciences and much more. The software is maintained and developed by academicians and professionals and as such, is continuously evolving and up to date. Statistics and Data with R presents an accessible guide to data manipulations, statistical analysis and graphics using R. Assuming no previous knowledge of statistics or R, the book includes: A comprehensive introduction to the R language. An integrated approach to importing and preparing data for analysis, exploring and analyzing the data, and presenting results. Over 300 examples, including detailed explanations of the R scripts used throughout. Over 100 moderately large data sets from disciplines ranging from Biology, Ecology and Environmental Science to Medicine, Law, Military and Social Sciences. A parallel discussion of analyses with the normal density, proportions (binomial), counts (Poisson) and bootstrap methods. Two extensive indexes that include references to every R function (and its arguments and packages used in the book) and to every introduced concept.
Handbook of Statistical Genomics by David J. Balding,Ida Moltke,John Marioni Pdf
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.
Mathematical and Statistical Methods for Genetic Analysis by Kenneth Lange Pdf
Written to equip students in the mathematical siences to understand and model the epidemiological and experimental data encountered in genetics research. This second edition expands the original edition by over 100 pages and includes new material. Sprinkled throughout the chapters are many new problems.
An Introduction to Statistical Genetic Data Analysis by Melinda C. Mills,Nicola Barban,Felix C. Tropf Pdf
A comprehensive introduction to modern applied statistical genetic data analysis, accessible to those without a background in molecular biology or genetics. Human genetic research is now relevant beyond biology, epidemiology, and the medical sciences, with applications in such fields as psychology, psychiatry, statistics, demography, sociology, and economics. With advances in computing power, the availability of data, and new techniques, it is now possible to integrate large-scale molecular genetic information into research across a broad range of topics. This book offers the first comprehensive introduction to modern applied statistical genetic data analysis that covers theory, data preparation, and analysis of molecular genetic data, with hands-on computer exercises. It is accessible to students and researchers in any empirically oriented medical, biological, or social science discipline; a background in molecular biology or genetics is not required. The book first provides foundations for statistical genetic data analysis, including a survey of fundamental concepts, primers on statistics and human evolution, and an introduction to polygenic scores. It then covers the practicalities of working with genetic data, discussing such topics as analytical challenges and data management. Finally, the book presents applications and advanced topics, including polygenic score and gene-environment interaction applications, Mendelian Randomization and instrumental variables, and ethical issues. The software and data used in the book are freely available and can be found on the book's website.
Computational Genomics with R by Altuna Akalin Pdf
Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.
Author : Nan M. Laird,Christoph Lange Publisher : Springer Science & Business Media Page : 226 pages File Size : 53,6 Mb Release : 2010-12-13 Category : Medical ISBN : 9781441973382
The Fundamentals of Modern Statistical Genetics by Nan M. Laird,Christoph Lange Pdf
This book covers the statistical models and methods that are used to understand human genetics, following the historical and recent developments of human genetics. Starting with Mendel’s first experiments to genome-wide association studies, the book describes how genetic information can be incorporated into statistical models to discover disease genes. All commonly used approaches in statistical genetics (e.g. aggregation analysis, segregation, linkage analysis, etc), are used, but the focus of the book is modern approaches to association analysis. Numerous examples illustrate key points throughout the text, both of Mendelian and complex genetic disorders. The intended audience is statisticians, biostatisticians, epidemiologists and quantitatively- oriented geneticists and health scientists wanting to learn about statistical methods for genetic analysis, whether to better analyze genetic data, or to pursue research in methodology. A background in intermediate level statistical methods is required. The authors include few mathematical derivations, and the exercises provide problems for students with a broad range of skill levels. No background in genetics is assumed.
Handbook of Statistical Genetics by David J. Balding,Martin Bishop,Chris Cannings Pdf
The Handbook for Statistical Genetics is widely regarded as the reference work in the field. However, the field has developed considerably over the past three years. In particular the modeling of genetic networks has advanced considerably via the evolution of microarray analysis. As a consequence the 3rd edition of the handbook contains a much expanded section on Network Modeling, including 5 new chapters covering metabolic networks, graphical modeling and inference and simulation of pedigrees and genealogies. Other chapters new to the 3rd edition include Human Population Genetics, Genome-wide Association Studies, Family-based Association Studies, Pharmacogenetics, Epigenetics, Ethic and Insurance. As with the second Edition, the Handbook includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between the chapters, tying the different areas together. With heavy use of up-to-date examples, real-life case studies and references to web-based resources, this continues to be must-have reference in a vital area of research. Edited by the leading international authorities in the field. David Balding - Department of Epidemiology & Public Health, Imperial College An advisor for our Probability & Statistics series, Professor Balding is also a previous Wiley author, having written Weight-of-Evidence for Forensic DNA Profiles, as well as having edited the two previous editions of HSG. With over 20 years teaching experience, he’s also had dozens of articles published in numerous international journals. Martin Bishop – Head of the Bioinformatics Division at the HGMP Resource Centre As well as the first two editions of HSG, Dr Bishop has edited a number of introductory books on the application of informatics to molecular biology and genetics. He is the Associate Editor of the journal Bioinformatics and Managing Editor of Briefings in Bioinformatics. Chris Cannings – Division of Genomic Medicine, University of Sheffield With over 40 years teaching in the area, Professor Cannings has published over 100 papers and is on the editorial board of many related journals. Co-editor of the two previous editions of HSG, he also authored a book on this topic.
Biostatistics for Human Genetic Epidemiology by Bertram K. C. Chan Pdf
The book illustrates how biostatistics may numerically summarize human genetic epidemiology using R, and may be used successfully to solve problems in quantitative Genetic Epidemiology Biostatistics for Human Genetic Epidemiology provides statistical methodologies and R recipes for human genetic epidemiologic problems. It begins by introducing all the necessary probabilistic and statistical foundations, before moving on to topics related human genetic epidemiology, with R codes illustrations for various examples. This clear and concise book covers human genetic epidemiology, using R in data analysis, including multivariate data analysis. It examines probabilistic and statistical theories for modeling human genetic epidemiology – leading the readers through an effective epidemiologic model, from simple to advanced levels. Classical mathematical, probabilistic, and statistical theory are thoroughly discussed and presented. This book also presents R as a calculator and using R in data analysis. Additionally, it covers Advanced Human Genetic Data Concepts, the Study of Human Genetic Variation, Manhattan Plots, as well as the Procedures for Multiple Comparison. Numerous Worked Examples are provided for illustrations of concepts and real-life applications. Biostatistics for Human Genetic Epidemiology is an ideal reference for professionals and students in Medicine (particularly in Preventive Medicine and Public Health Medical Practices), as well as in Genetics, Epidemiology, and Biostatistics.
Statistical Learning in Genetics by Daniel Sorensen Pdf
This book provides an introduction to computer-based methods for the analysis of genomic data. Breakthroughs in molecular and computational biology have contributed to the emergence of vast data sets, where millions of genetic markers for each individual are coupled with medical records, generating an unparalleled resource for linking human genetic variation to human biology and disease. Similar developments have taken place in animal and plant breeding, where genetic marker information is combined with production traits. An important task for the statistical geneticist is to adapt, construct and implement models that can extract information from these large-scale data. An initial step is to understand the methodology that underlies the probability models and to learn the modern computer-intensive methods required for fitting these models. The objective of this book, suitable for readers who wish to develop analytic skills to perform genomic research, is to provide guidance to take this first step. This book is addressed to numerate biologists who typically lack the formal mathematical background of the professional statistician. For this reason, considerably more detail in explanations and derivations is offered. It is written in a concise style and examples are used profusely. A large proportion of the examples involve programming with the open-source package R. The R code needed to solve the exercises is provided. The MarkDown interface allows the students to implement the code on their own computer, contributing to a better understanding of the underlying theory. Part I presents methods of inference based on likelihood and Bayesian methods, including computational techniques for fitting likelihood and Bayesian models. Part II discusses prediction for continuous and binary data using both frequentist and Bayesian approaches. Some of the models used for prediction are also used for gene discovery. The challenge is to find promising genes without incurring a large proportion of false positive results. Therefore, Part II includes a detour on False Discovery Rate assuming frequentist and Bayesian perspectives. The last chapter of Part II provides an overview of a selected number of non-parametric methods. Part III consists of exercises and their solutions. Daniel Sorensen holds PhD and DSc degrees from the University of Edinburgh and is an elected Fellow of the American Statistical Association. He was professor of Statistical Genetics at Aarhus University where, at present, he is professor emeritus.
Statistics in Human Genetics and Molecular Biology by Cavan Reilly Pdf
Focusing on the roles of different segments of DNA, Statistics in Human Genetics and Molecular Biology provides a basic understanding of problems arising in the analysis of genetics and genomics. It presents statistical applications in genetic mapping, DNA/protein sequence alignment, and analyses of gene expression data from microarray experiments.
Applied Statistics with R by Justin C. Touchon Pdf
This book uses the statistical language R, which is the choice of ecologists worldwide and is rapidly becoming the 'go-to' stats program throughout the life-sciences. Furthermore, by using a single, real-world dataset throughout the book, readers are encouraged to become deeply familiar with an imperfect but realistic set of data. - -
The high-level language of R is recognized as one of the mostpowerful and flexible statistical software environments, and israpidly becoming the standard setting for quantitative analysis,statistics and graphics. R provides free access to unrivalledcoverage and cutting-edge applications, enabling the user to applynumerous statistical methods ranging from simple regression to timeseries or multivariate analysis. Building on the success of the author’s bestsellingStatistics: An Introduction using R, The R Book ispacked with worked examples, providing an all inclusive guide to R,ideal for novice and more accomplished users alike. The bookassumes no background in statistics or computing and introduces theadvantages of the R environment, detailing its applications in awide range of disciplines. Provides the first comprehensive reference manual for the Rlanguage, including practical guidance and full coverage of thegraphics facilities. Introduces all the statistical models covered by R, beginningwith simple classical tests such as chi-square and t-test. Proceeds to examine more advance methods, from regression andanalysis of variance, through to generalized linear models,generalized mixed models, time series, spatial statistics,multivariate statistics and much more. The R Book is aimed at undergraduates, postgraduates andprofessionals in science, engineering and medicine. It is alsoideal for students and professionals in statistics, economics,geography and the social sciences.
Population Genomics with R by Emmanuel Paradis Pdf
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).
