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| statistical bioinformatics with r: Statistical Bioinformatics with R Sunil K. Mathur, 2009-12-21 Statistical Bioinformatics provides a balanced treatment of statistical theory in the context of bioinformatics applications. Designed for a one or two semester senior undergraduate or graduate bioinformatics course, the text takes a broad view of the subject – not just gene expression and sequence analysis, but a careful balance of statistical theory in the context of bioinformatics applications. The inclusion of R & SAS code as well as the development of advanced methodology such as Bayesian and Markov models provides students with the important foundation needed to conduct bioinformatics. - Integrates biological, statistical and computational concepts - Inclusion of R & SAS code - Provides coverage of complex statistical methods in context with applications in bioinformatics - Exercises and examples aid teaching and learning presented at the right level - Bayesian methods and the modern multiple testing principles in one convenient book |
| statistical bioinformatics with r: Modern Statistics for Modern Biology SUSAN. HUBER HOLMES (WOLFGANG.), Wolfgang Huber, 2018 |
| statistical bioinformatics with r: R Programming for Bioinformatics Robert Gentleman, 2008-07-14 Due to its data handling and modeling capabilities as well as its flexibility, R is becoming the most widely used software in bioinformatics. R Programming for Bioinformatics explores the programming skills needed to use this software tool for the solution of bioinformatics and computational biology problems. Drawing on the author’s first-hand experiences as an expert in R, the book begins with coverage on the general properties of the R language, several unique programming aspects of R, and object-oriented programming in R. It presents methods for data input and output as well as database interactions. The author also examines different facets of string handling and manipulations, discusses the interfacing of R with other languages, and describes how to write software packages. He concludes with a discussion on the debugging and profiling of R code. With numerous examples and exercises, this practical guide focuses on developing R programming skills in order to tackle problems encountered in bioinformatics and computational biology. |
| statistical bioinformatics with r: Statistical Bioinformatics Jae K. Lee, 2011-09-20 This book provides an essential understanding of statistical concepts necessary for the analysis of genomic and proteomic data using computational techniques. The author presents both basic and advanced topics, focusing on those that are relevant to the computational analysis of large data sets in biology. Chapters begin with a description of a statistical concept and a current example from biomedical research, followed by more detailed presentation, discussion of limitations, and problems. The book starts with an introduction to probability and statistics for genome-wide data, and moves into topics such as clustering, classification, multi-dimensional visualization, experimental design, statistical resampling, and statistical network analysis. Clearly explains the use of bioinformatics tools in life sciences research without requiring an advanced background in math/statistics Enables biomedical and life sciences researchers to successfully evaluate the validity of their results and make inferences Enables statistical and quantitative researchers to rapidly learn novel statistical concepts and techniques appropriate for large biological data analysis Carefully revisits frequently used statistical approaches and highlights their limitations in large biological data analysis Offers programming examples and datasets Includes chapter problem sets, a glossary, a list of statistical notations, and appendices with references to background mathematical and technical material Features supplementary materials, including datasets, links, and a statistical package available online Statistical Bioinformatics is an ideal textbook for students in medicine, life sciences, and bioengineering, aimed at researchers who utilize computational tools for the analysis of genomic, proteomic, and many other emerging high-throughput molecular data. It may also serve as a rapid introduction to the bioinformatics science for statistical and computational students and audiences who have not experienced such analysis tasks before. |
| statistical bioinformatics with r: Bioinformatics and Computational Biology Solutions Using R and Bioconductor Robert Gentleman, 2005-08-31 Full four-color book. Some of the editors created the Bioconductor project and Robert Gentleman is one of the two originators of R. All methods are illustrated with publicly available data, and a major section of the book is devoted to fully worked case studies. Code underlying all of the computations that are shown is made available on a companion website, and readers can reproduce every number, figure, and table on their own computers. |
| statistical bioinformatics with r: The R Software Pierre Lafaye de Micheaux, Rémy Drouilhet, Benoit Liquet, 2014-05-13 The contents of The R Software are presented so as to be both comprehensive and easy for the reader to use. Besides its application as a self-learning text, this book can support lectures on R at any level from beginner to advanced. This book can serve as a textbook on R for beginners as well as more advanced users, working on Windows, MacOs or Linux OSes. The first part of the book deals with the heart of the R language and its fundamental concepts, including data organization, import and export, various manipulations, documentation, plots, programming and maintenance. The last chapter in this part deals with oriented object programming as well as interfacing R with C/C++ or Fortran, and contains a section on debugging techniques. This is followed by the second part of the book, which provides detailed explanations on how to perform many standard statistical analyses, mainly in the Biostatistics field. Topics from mathematical and statistical settings that are included are matrix operations, integration, optimization, descriptive statistics, simulations, confidence intervals and hypothesis testing, simple and multiple linear regression, and analysis of variance. Each statistical chapter in the second part relies on one or more real biomedical data sets, kindly made available by the Bordeaux School of Public Health (Institut de Santé Publique, d'Épidémiologie et de Développement - ISPED) and described at the beginning of the book. Each chapter ends with an assessment section: memorandum of most important terms, followed by a section of theoretical exercises (to be done on paper), which can be used as questions for a test. Moreover, worksheets enable the reader to check his new abilities in R. Solutions to all exercises and worksheets are included in this book. |
| statistical bioinformatics with r: Statistical Bioinformatics with R Sunil K. Mathur, 2010 Designed for a one or two semester senior undergraduate or graduate bioinformatics course, Statistical Bioinformatics takes a broad view of the subject - not just gene expression and sequence analysis, but a careful balance of statistical theory in the context of bioinformatics applications. The inclusion of R code as well as the development of advanced methodology such as Bayesian and Markov models provides students with the important foundation needed to conduct bioinformatics. Ancillary list: * Online ISM- http://textbooks.elsevier.com/web/manuals.aspx?isbn=9780123751041 * Companion Website w/ R code and Ebook- http://textbooks.elsevier.com/web/manuals.aspx?isbn=9780123751041 * Powerpoint slides- http://textbooks.elsevier.com/web/Manuals.aspx?isbn=9780123751041 Integrates biological, statistical and computational concepts Inclusion of R & SAS code Provides coverage of complex statistical methods in context with applications in bioinformatics Exercises and examples aid teaching and learning presented at the right level Bayesian methods and the modern multiple testing principles in one convenient book |
| statistical bioinformatics with r: R for Data Science Hadley Wickham, Garrett Grolemund, 2016-12-12 Learn how to use R to turn raw data into insight, knowledge, and understanding. This book introduces you to R, RStudio, and the tidyverse, a collection of R packages designed to work together to make data science fast, fluent, and fun. Suitable for readers with no previous programming experience, R for Data Science is designed to get you doing data science as quickly as possible. Authors Hadley Wickham and Garrett Grolemund guide you through the steps of importing, wrangling, exploring, and modeling your data and communicating the results. You'll get a complete, big-picture understanding of the data science cycle, along with basic tools you need to manage the details. Each section of the book is paired with exercises to help you practice what you've learned along the way. You'll learn how to: Wrangle—transform your datasets into a form convenient for analysis Program—learn powerful R tools for solving data problems with greater clarity and ease Explore—examine your data, generate hypotheses, and quickly test them Model—provide a low-dimensional summary that captures true signals in your dataset Communicate—learn R Markdown for integrating prose, code, and results |
| statistical bioinformatics with r: Statistical Analysis of Network Data with R Eric D. Kolaczyk, Gábor Csárdi, 2014-05-22 Networks have permeated everyday life through everyday realities like the Internet, social networks, and viral marketing. As such, network analysis is an important growth area in the quantitative sciences, with roots in social network analysis going back to the 1930s and graph theory going back centuries. Measurement and analysis are integral components of network research. As a result, statistical methods play a critical role in network analysis. This book is the first of its kind in network research. It can be used as a stand-alone resource in which multiple R packages are used to illustrate how to conduct a wide range of network analyses, from basic manipulation and visualization, to summary and characterization, to modeling of network data. The central package is igraph, which provides extensive capabilities for studying network graphs in R. This text builds on Eric D. Kolaczyk’s book Statistical Analysis of Network Data (Springer, 2009). |
| statistical bioinformatics with r: Bioinformatics with R Cookbook Paurush Praveen, Paurush Praveen Sinha, 2014 This book is an easy-to-follow, stepwise guide to handle real life Bioinformatics problems. Each recipe comes with a detailed explanation to the solution steps. A systematic approach, coupled with lots of illustrations, tips, and tricks will help you as a reader grasp even the trickiest of concepts without difficulty. This book is ideal for computational biologists and bioinformaticians with basic knowledge of R programming, bioinformatics and statistics. If you want to understand various critical concepts needed to develop your computational models in Bioinformatics, then this book is for you. |
| statistical bioinformatics with r: Computational Genomics with R Altuna Akalin, 2020-12-16 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. |
| statistical bioinformatics with r: Statistical Shape Analysis Ian L. Dryden, Kanti V. Mardia, 2016-06-28 A thoroughly revised and updated edition of this introduction to modern statistical methods for shape analysis Shape analysis is an important tool in the many disciplines where objects are compared using geometrical features. Examples include comparing brain shape in schizophrenia; investigating protein molecules in bioinformatics; and describing growth of organisms in biology. This book is a significant update of the highly-regarded Statistical Shape Analysis by the same authors. The new edition lays the foundations of landmark shape analysis, including geometrical concepts and statistical techniques, and extends to include analysis of curves, surfaces, images and other types of object data. Key definitions and concepts are discussed throughout, and the relative merits of different approaches are presented. The authors have included substantial new material on recent statistical developments and offer numerous examples throughout the text. Concepts are introduced in an accessible manner, while retaining sufficient detail for more specialist statisticians to appreciate the challenges and opportunities of this new field. Computer code has been included for instructional use, along with exercises to enable readers to implement the applications themselves in R and to follow the key ideas by hands-on analysis. Offers a detailed yet accessible treatment of statistical methods for shape analysis Includes numerous examples and applications from many disciplines Provides R code for implementing the examples Covers a wide variety of recent developments in shape analysis Shape Analysis, with Applications in R will offer a valuable introduction to this fast-moving research area for statisticians and other applied scientists working in diverse areas, including archaeology, bioinformatics, biology, chemistry, computer science, medicine, morphometics and image analysis. |
| statistical bioinformatics with r: Statistics and Data Analysis for Microarrays Using R and Bioconductor Sorin Draghici, 2016-04-19 Richly illustrated in color, Statistics and Data Analysis for Microarrays Using R and Bioconductor, Second Edition provides a clear and rigorous description of powerful analysis techniques and algorithms for mining and interpreting biological information. Omitting tedious details, heavy formalisms, and cryptic notations, the text takes a hands-on, example-based approach that teaches students the basics of R and microarray technology as well as how to choose and apply the proper data analysis tool to specific problems. New to the Second EditionCompletely updated and double the size of its predecessor, this timely second edition replaces the commercial software with the open source R and Bioconductor environments. Fourteen new chapters cover such topics as the basic mechanisms of the cell, reliability and reproducibility issues in DNA microarrays, basic statistics and linear models in R, experiment design, multiple comparisons, quality control, data pre-processing and normalization, Gene Ontology analysis, pathway analysis, and machine learning techniques. Methods are illustrated with toy examples and real data and the R code for all routines is available on an accompanying downloadable resource. With all the necessary prerequisites included, this best-selling book guides students from very basic notions to advanced analysis techniques in R and Bioconductor. The first half of the text presents an overview of microarrays and the statistical elements that form the building blocks of any data analysis. The second half introduces the techniques most commonly used in the analysis of microarray data. |
| statistical bioinformatics with r: An Introduction to Statistical Learning Gareth James, Daniela Witten, Trevor Hastie, Robert Tibshirani, Jonathan Taylor, 2023-06-30 An Introduction to Statistical Learning provides an accessible overview of the field of statistical learning, an essential toolset for making sense of the vast and complex data sets that have emerged in fields ranging from biology to finance, marketing, and astrophysics in the past twenty years. This book presents some of the most important modeling and prediction techniques, along with relevant applications. Topics include linear regression, classification, resampling methods, shrinkage approaches, tree-based methods, support vector machines, clustering, deep learning, survival analysis, multiple testing, and more. Color graphics and real-world examples are used to illustrate the methods presented. This book is targeted at statisticians and non-statisticians alike, who wish to use cutting-edge statistical learning techniques to analyze their data. Four of the authors co-wrote An Introduction to Statistical Learning, With Applications in R (ISLR), which has become a mainstay of undergraduate and graduate classrooms worldwide, as well as an important reference book for data scientists. One of the keys to its success was that each chapter contains a tutorial on implementing the analyses and methods presented in the R scientific computing environment. However, in recent years Python has become a popular language for data science, and there has been increasing demand for a Python-based alternative to ISLR. Hence, this book (ISLP) covers the same materials as ISLR but with labs implemented in Python. These labs will be useful both for Python novices, as well as experienced users. |
| statistical bioinformatics with r: Data Analysis for the Life Sciences with R Rafael A. Irizarry, Michael I. Love, 2016-10-04 This book covers several of the statistical concepts and data analytic skills needed to succeed in data-driven life science research. The authors proceed from relatively basic concepts related to computed p-values to advanced topics related to analyzing highthroughput data. They include the R code that performs this analysis and connect the lines of code to the statistical and mathematical concepts explained. |
| statistical bioinformatics with r: New Statistics with R Andy Hector, 2015 An introductory level text covering linear, generalized linear, linear mixed-effects, and generalized mixed models implemented in R and set within a contemporary framework. |
| statistical bioinformatics with r: Metaprogramming in R Thomas Mailund, 2017-06-01 Learn how to manipulate functions and expressions to modify how the R language interprets itself. This book is an introduction to metaprogramming in the R language, so you will write programs to manipulate other programs. Metaprogramming in R shows you how to treat code as data that you can generate, analyze, or modify. R is a very high-level language where all operations are functions and all functions are data that can be manipulated. This book shows you how to leverage R's natural flexibility in how function calls and expressions are evaluated, to create small domain-specific languages to extend R within the R language itself. What You'll Learn Find out about the anatomy of a function in R Look inside a function call Work with R expressions and environments Manipulate expressions in R Use substitutions Who This Book Is For Those with at least some experience with R and certainly for those with experience in other programming languages. |
| statistical bioinformatics with r: R Bioinformatics Cookbook Dan MacLean, 2019-10-11 Over 60 recipes to model and handle real-life biological data using modern libraries from the R ecosystem Key Features Apply modern R packages to handle biological data using real-world examples Represent biological data with advanced visualizations suitable for research and publications Handle real-world problems in bioinformatics such as next-generation sequencing, metagenomics, and automating analyses Book Description Handling biological data effectively requires an in-depth knowledge of machine learning techniques and computational skills, along with an understanding of how to use tools such as edgeR and DESeq. With the R Bioinformatics Cookbook, you'll explore all this and more, tackling common and not-so-common challenges in the bioinformatics domain using real-world examples. This book will use a recipe-based approach to show you how to perform practical research and analysis in computational biology with R. You will learn how to effectively analyze your data with the latest tools in Bioconductor, ggplot, and tidyverse. The book will guide you through the essential tools in Bioconductor to help you understand and carry out protocols in RNAseq, phylogenetics, genomics, and sequence analysis. As you progress, you will get up to speed with how machine learning techniques can be used in the bioinformatics domain. You will gradually develop key computational skills such as creating reusable workflows in R Markdown and packages for code reuse. By the end of this book, you'll have gained a solid understanding of the most important and widely used techniques in bioinformatic analysis and the tools you need to work with real biological data. What you will learn Employ Bioconductor to determine differential expressions in RNAseq data Run SAMtools and develop pipelines to find single nucleotide polymorphisms (SNPs) and Indels Use ggplot to create and annotate a range of visualizations Query external databases with Ensembl to find functional genomics information Execute large-scale multiple sequence alignment with DECIPHER to perform comparative genomics Use d3.js and Plotly to create dynamic and interactive web graphics Use k-nearest neighbors, support vector machines and random forests to find groups and classify data Who this book is for This book is for bioinformaticians, data analysts, researchers, and R developers who want to address intermediate-to-advanced biological and bioinformatics problems by learning through a recipe-based approach. Working knowledge of R programming language and basic knowledge of bioinformatics are prerequisites. |
| statistical bioinformatics with r: Introductory Statistics with R Peter Dalgaard, 2006-04-06 This book provides an elementary-level introduction to R, targeting both non-statistician scientists in various fields and students of statistics. The main mode of presentation is via code examples with liberal commenting of the code and the output, from the computational as well as the statistical viewpoint. Brief sections introduce the statistical methods before they are used. A supplementary R package can be downloaded and contains the data sets. All examples are directly runnable and all graphics in the text are generated from the examples. The statistical methodology covered includes statistical standard distributions, one- and two-sample tests with continuous data, regression analysis, one-and two-way analysis of variance, regression analysis, analysis of tabular data, and sample size calculations. In addition, the last four chapters contain introductions to multiple linear regression analysis, linear models in general, logistic regression, and survival analysis. |
| statistical bioinformatics with r: R For Dummies Andrie de Vries, Joris Meys, 2012-06-06 Master the programming language of choice among statisticians and data analysts worldwide Coming to grips with R can be tough, even for seasoned statisticians and data analysts. Enter R For Dummies, the quick, easy way to master all the R you'll ever need. Requiring no prior programming experience and packed with practical examples, easy, step-by-step exercises, and sample code, this extremely accessible guide is the ideal introduction to R for complete beginners. It also covers many concepts that intermediate-level programmers will find extremely useful. Master your R ABCs ? get up to speed in no time with the basics, from installing and configuring R to writing simple scripts and performing simultaneous calculations on many variables Put data in its place ? get to know your way around lists, data frames, and other R data structures while learning to interact with other programs, such as Microsoft Excel Make data dance to your tune ? learn how to reshape and manipulate data, merge data sets, split and combine data, perform calculations on vectors and arrays, and much more Visualize it ? learn to use R's powerful data visualization features to create beautiful and informative graphical presentations of your data Get statistical ? find out how to do simple statistical analysis, summarize your variables, and conduct classic statistical tests, such as t-tests Expand and customize R ? get the lowdown on how to find, install, and make the most of add-on packages created by the global R community for a wide variety of purposes Open the book and find: Help downloading, installing, and configuring R Tips for getting data in and out of R Ways to use data frames and lists to organize data How to manipulate and process data Advice on fitting regression models and ANOVA Helpful hints for working with graphics How to code in R What R mailing lists and forums can do for you |
| statistical bioinformatics with r: Bioinformatics Data Skills Vince Buffalo, 2015-07 Learn the data skills necessary for turning large sequencing datasets into reproducible and robust biological findings. With this practical guide, youâ??ll learn how to use freely available open source tools to extract meaning from large complex biological data sets. At no other point in human history has our ability to understand lifeâ??s complexities been so dependent on our skills to work with and analyze data. This intermediate-level book teaches the general computational and data skills you need to analyze biological data. If you have experience with a scripting language like Python, youâ??re ready to get started. Go from handling small problems with messy scripts to tackling large problems with clever methods and tools Process bioinformatics data with powerful Unix pipelines and data tools Learn how to use exploratory data analysis techniques in the R language Use efficient methods to work with genomic range data and range operations Work with common genomics data file formats like FASTA, FASTQ, SAM, and BAM Manage your bioinformatics project with the Git version control system Tackle tedious data processing tasks with with Bash scripts and Makefiles |
| statistical bioinformatics with r: Molecular Data Analysis Using R Csaba Ortutay, Zsuzsanna Ortutay, 2017-02-06 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. |
| statistical bioinformatics with r: Advanced R Statistical Programming and Data Models Matt Wiley, Joshua F. Wiley, 2019-02-20 Carry out a variety of advanced statistical analyses including generalized additive models, mixed effects models, multiple imputation, machine learning, and missing data techniques using R. Each chapter starts with conceptual background information about the techniques, includes multiple examples using R to achieve results, and concludes with a case study. Written by Matt and Joshua F. Wiley, Advanced R Statistical Programming and Data Models shows you how to conduct data analysis using the popular R language. You’ll delve into the preconditions or hypothesis for various statistical tests and techniques and work through concrete examples using R for a variety of these next-level analytics. This is a must-have guide and reference on using and programming with the R language. What You’ll Learn Conduct advanced analyses in R including: generalized linear models, generalized additive models, mixedeffects models, machine learning, and parallel processing Carry out regression modeling using R data visualization, linear and advanced regression, additive models, survival / time to event analysis Handle machine learning using R including parallel processing, dimension reduction, and feature selection and classification Address missing data using multiple imputation in R Work on factor analysis, generalized linear mixed models, and modeling intraindividual variability Who This Book Is For Working professionals, researchers, or students who are familiar with R and basic statistical techniques such as linear regression and who want to learn how to use R to perform more advanced analytics. Particularly, researchers and data analysts in the social sciences may benefit from these techniques. Additionally, analysts who need parallel processing to speed up analytics are givenproven code to reduce time to result(s). |
| statistical bioinformatics with r: Microarray Bioinformatics Dov Stekel, 2003-09-08 This book is a comprehensive guide to all of the mathematics, statistics and computing you will need to successfully operate DNA microarray experiments. It is written for researchers, clinicians, laboratory heads and managers, from both biology and bioinformatics backgrounds, who work with, or who intend to work with microarrays. The book covers all aspects of microarray bioinformatics, giving you the tools to design arrays and experiments, to analyze your data, and to share your results with your organisation or with the international community. There are chapters covering sequence databases, oligonucleotide design, experimental design, image processing, normalisation, identifying differentially expressed genes, clustering, classification and data standards. The book is based on the highly successful Microarray Bioinformatics course at Oxford University, and therefore is ideally suited for teaching the subject at postgraduate or professional level. |
| statistical bioinformatics with r: A First Course in Statistical Programming with R John Braun, Duncan James Murdoch, 2007 The only introduction you'll need to start programming in R. |
| statistical bioinformatics with r: Regression Modeling Strategies Frank E. Harrell, 2013-03-09 Many texts are excellent sources of knowledge about individual statistical tools, but the art of data analysis is about choosing and using multiple tools. Instead of presenting isolated techniques, this text emphasizes problem solving strategies that address the many issues arising when developing multivariable models using real data and not standard textbook examples. It includes imputation methods for dealing with missing data effectively, methods for dealing with nonlinear relationships and for making the estimation of transformations a formal part of the modeling process, methods for dealing with too many variables to analyze and not enough observations, and powerful model validation techniques based on the bootstrap. This text realistically deals with model uncertainty and its effects on inference to achieve safe data mining. |
| statistical bioinformatics with r: Applied Statistical Genetics with R Andrea S. Foulkes, 2009-04-17 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. |
| statistical bioinformatics with r: Biostatistics with R Jan Lepš, Petr Šmilauer, 2020-07-30 A straightforward introduction to a wide range of statistical methods for field biologists, using thoroughly explained R code. |
| statistical bioinformatics with r: The Elements of Statistical Learning Trevor Hastie, Robert Tibshirani, Jerome Friedman, 2013-11-11 During the past decade there has been an explosion in computation and information technology. With it have come vast amounts of data in a variety of fields such as medicine, biology, finance, and marketing. The challenge of understanding these data has led to the development of new tools in the field of statistics, and spawned new areas such as data mining, machine learning, and bioinformatics. Many of these tools have common underpinnings but are often expressed with different terminology. This book describes the important ideas in these areas in a common conceptual framework. While the approach is statistical, the emphasis is on concepts rather than mathematics. Many examples are given, with a liberal use of color graphics. It is a valuable resource for statisticians and anyone interested in data mining in science or industry. The book's coverage is broad, from supervised learning (prediction) to unsupervised learning. The many topics include neural networks, support vector machines, classification trees and boosting---the first comprehensive treatment of this topic in any book. This major new edition features many topics not covered in the original, including graphical models, random forests, ensemble methods, least angle regression & path algorithms for the lasso, non-negative matrix factorization, and spectral clustering. There is also a chapter on methods for ``wide'' data (p bigger than n), including multiple testing and false discovery rates. |
| statistical bioinformatics with r: A Handbook of Statistical Analyses Using R, Second Edition Torsten Hothorn, Brian S. Everitt, 2009-07-20 A Proven Guide for Easily Using R to Effectively Analyze Data Like its bestselling predecessor, A Handbook of Statistical Analyses Using R, Second Edition provides a guide to data analysis using the R system for statistical computing. Each chapter includes a brief account of the relevant statistical background, along with appropriate references. New to the Second Edition New chapters on graphical displays, generalized additive models, and simultaneous inference A new section on generalized linear mixed models that completes the discussion on the analysis of longitudinal data where the response variable does not have a normal distribution New examples and additional exercises in several chapters A new version of the HSAUR package (HSAUR2), which is available from CRAN This edition continues to offer straightforward descriptions of how to conduct a range of statistical analyses using R, from simple inference to recursive partitioning to cluster analysis. Focusing on how to use R and interpret the results, it provides students and researchers in many disciplines with a self-contained means of using R to analyze their data. |
| statistical bioinformatics with r: Spatio-temporal Statistics with R Christopher K. Wikle, Andrew Zammit-Mangion, Noel A. C. Cressie, 2019 Spatio-Temporal Statistics with R provides an accessible introduction to statistical analysis of spatio-temporal data, with hands-on applications of the statistical methods using R Labs found at the end of each chapter. |
| statistical bioinformatics with r: Statistical Analysis of Network Data Eric D. Kolaczyk, 2010-12-06 In recent years there has been an explosion of network data – that is, measu- ments that are either of or from a system conceptualized as a network – from se- ingly all corners of science. The combination of an increasingly pervasive interest in scienti c analysis at a systems level and the ever-growing capabilities for hi- throughput data collection in various elds has fueled this trend. Researchers from biology and bioinformatics to physics, from computer science to the information sciences, and from economics to sociology are more and more engaged in the c- lection and statistical analysis of data from a network-centric perspective. Accordingly, the contributions to statistical methods and modeling in this area have come from a similarly broad spectrum of areas, often independently of each other. Many books already have been written addressing network data and network problems in speci c individual disciplines. However, there is at present no single book that provides a modern treatment of a core body of knowledge for statistical analysis of network data that cuts across the various disciplines and is organized rather according to a statistical taxonomy of tasks and techniques. This book seeks to ll that gap and, as such, it aims to contribute to a growing trend in recent years to facilitate the exchange of knowledge across the pre-existing boundaries between those disciplines that play a role in what is coming to be called ‘network science. |
| statistical bioinformatics with r: Introduction to Bioinformatics with R Edward Curry, 2020-11-02 In biological research, the amount of data available to researchers has increased so much over recent years, it is becoming increasingly difficult to understand the current state of the art without some experience and understanding of data analytics and bioinformatics. An Introduction to Bioinformatics with R: A Practical Guide for Biologists leads the reader through the basics of computational analysis of data encountered in modern biological research. With no previous experience with statistics or programming required, readers will develop the ability to plan suitable analyses of biological datasets, and to use the R programming environment to perform these analyses. This is achieved through a series of case studies using R to answer research questions using molecular biology datasets. Broadly applicable statistical methods are explained, including linear and rank-based correlation, distance metrics and hierarchical clustering, hypothesis testing using linear regression, proportional hazards regression for survival data, and principal component analysis. These methods are then applied as appropriate throughout the case studies, illustrating how they can be used to answer research questions. Key Features: · Provides a practical course in computational data analysis suitable for students or researchers with no previous exposure to computer programming. · Describes in detail the theoretical basis for statistical analysis techniques used throughout the textbook, from basic principles · Presents walk-throughs of data analysis tasks using R and example datasets. All R commands are presented and explained in order to enable the reader to carry out these tasks themselves. · Uses outputs from a large range of molecular biology platforms including DNA methylation and genotyping microarrays; RNA-seq, genome sequencing, ChIP-seq and bisulphite sequencing; and high-throughput phenotypic screens. · Gives worked-out examples geared towards problems encountered in cancer research, which can also be applied across many areas of molecular biology and medical research. This book has been developed over years of training biological scientists and clinicians to analyse the large datasets available in their cancer research projects. It is appropriate for use as a textbook or as a practical book for biological scientists looking to gain bioinformatics skills. |
| statistical bioinformatics with r: Handbook of Statistical Bioinformatics Henry Horng-Shing Lu, Bernhard Schölkopf, Hongyu Zhao, 2011-05-17 Numerous fascinating breakthroughs in biotechnology have generated large volumes and diverse types of high throughput data that demand the development of efficient and appropriate tools in computational statistics integrated with biological knowledge and computational algorithms. This volume collects contributed chapters from leading researchers to survey the many active research topics and promote the visibility of this research area. This volume is intended to provide an introductory and reference book for students and researchers who are interested in the recent developments of computational statistics in computational biology. |
| statistical bioinformatics with r: Tree-Based Methods for Statistical Learning in R Brandon M. Greenwell, 2022-06-23 Tree-based Methods for Statistical Learning in R provides a thorough introduction to both individual decision tree algorithms (Part I) and ensembles thereof (Part II). Part I of the book brings several different tree algorithms into focus, both conventional and contemporary. Building a strong foundation for how individual decision trees work will help readers better understand tree-based ensembles at a deeper level, which lie at the cutting edge of modern statistical and machine learning methodology. The book follows up most ideas and mathematical concepts with code-based examples in the R statistical language; with an emphasis on using as few external packages as possible. For example, users will be exposed to writing their own random forest and gradient tree boosting functions using simple for loops and basic tree fitting software (like rpart and party/partykit), and more. The core chapters also end with a detailed section on relevant software in both R and other opensource alternatives (e.g., Python, Spark, and Julia), and example usage on real data sets. While the book mostly uses R, it is meant to be equally accessible and useful to non-R programmers. Consumers of this book will have gained a solid foundation (and appreciation) for tree-based methods and how they can be used to solve practical problems and challenges data scientists often face in applied work. Features: Thorough coverage, from the ground up, of tree-based methods (e.g., CART, conditional inference trees, bagging, boosting, and random forests). A companion website containing additional supplementary material and the code to reproduce every example and figure in the book. A companion R package, called treemisc, which contains several data sets and functions used throughout the book (e.g., there’s an implementation of gradient tree boosting with LAD loss that shows how to perform the line search step by updating the terminal node estimates of a fitted rpart tree). Interesting examples that are of practical use; for example, how to construct partial dependence plots from a fitted model in Spark MLlib (using only Spark operations), or post-processing tree ensembles via the LASSO to reduce the number of trees while maintaining, or even improving performance. |
| statistical bioinformatics with r: Applied Biclustering Methods for Big and High-Dimensional Data Using R Adetayo Kasim, Ziv Shkedy, Sebastian Kaiser, Sepp Hochreiter, Willem Talloen, 2016-08-18 Proven Methods for Big Data Analysis As big data has become standard in many application areas, challenges have arisen related to methodology and software development, including how to discover meaningful patterns in the vast amounts of data. Addressing these problems, Applied Biclustering Methods for Big and High-Dimensional Data Using R shows how to apply biclustering methods to find local patterns in a big data matrix. The book presents an overview of data analysis using biclustering methods from a practical point of view. Real case studies in drug discovery, genetics, marketing research, biology, toxicity, and sports illustrate the use of several biclustering methods. References to technical details of the methods are provided for readers who wish to investigate the full theoretical background. All the methods are accompanied with R examples that show how to conduct the analyses. The examples, software, and other materials are available on a supplementary website. |
| statistical bioinformatics with r: Topics in Applied Statistics Mingxiu Hu, Yi Liu, Jianchang Lin, 2013-09-14 This volume presents 27 selected papers in topics that range from statistical applications in business and finance to applications in clinical trials and biomarker analysis. All papers feature original, peer-reviewed content. The editors intentionally selected papers that cover many topics so that the volume will serve the whole statistical community and a variety of research interests. The papers represent select contributions to the 21st ICSA Applied Statistics Symposium. The International Chinese Statistical Association (ICSA) Symposium took place between the 23rd and 26th of June, 2012 in Boston, Massachusetts. It was co-sponsored by the International Society for Biopharmaceutical Statistics (ISBS) and American Statistical Association (ASA). This is the inaugural proceedings volume to share research from the ICSA Applied Statistics Symposium. |
| statistical bioinformatics with r: Scientific Data Management Arie Shoshani, Doron Rotem, 2009-12-16 Dealing with the volume, complexity, and diversity of data currently being generated by scientific experiments and simulations often causes scientists to waste productive time. Scientific Data Management: Challenges, Technology, and Deployment describes cutting-edge technologies and solutions for managing and analyzing vast amounts of data, helping |
| statistical bioinformatics with r: Handbook of Statistical Systems Biology Michael Stumpf, David J. Balding, Mark Girolami, 2011-09-09 Systems Biology is now entering a mature phase in which the key issues are characterising uncertainty and stochastic effects in mathematical models of biological systems. The area is moving towards a full statistical analysis and probabilistic reasoning over the inferences that can be made from mathematical models. This handbook presents a comprehensive guide to the discipline for practitioners and educators, in providing a full and detailed treatment of these important and emerging subjects. Leading experts in systems biology and statistics have come together to provide insight in to the major ideas in the field, and in particular methods of specifying and fitting models, and estimating the unknown parameters. This book: Provides a comprehensive account of inference techniques in systems biology. Introduces classical and Bayesian statistical methods for complex systems. Explores networks and graphical modeling as well as a wide range of statistical models for dynamical systems. Discusses various applications for statistical systems biology, such as gene regulation and signal transduction. Features statistical data analysis on numerous technologies, including metabolic and transcriptomic technologies. Presents an in-depth presentation of reverse engineering approaches. Provides colour illustrations to explain key concepts. This handbook will be a key resource for researchers practising systems biology, and those requiring a comprehensive overview of this important field. |
| statistical bioinformatics with r: Evidential Statistics, Model Identification, and Science Mark Louis Taper, Jose Miguel Ponciano, Yukihiko Toquenaga, Hidetoshi Shimodaira, 2022-02-15 |
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