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Bioconductor Case Studies
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Book Synopsis Bioconductor Case Studies by : Florian Hahne
Download or read book Bioconductor Case Studies written by Florian Hahne and published by Springer Science & Business Media. This book was released on 2010-06-09 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioconductor software has become a standard tool for the analysis and comprehension of data from high-throughput genomics experiments. Its application spans a broad field of technologies used in contemporary molecular biology. In this volume, the authors present a collection of cases to apply Bioconductor tools in the analysis of microarray gene expression data. Topics covered include: (1) import and preprocessing of data from various sources; (2) statistical modeling of differential gene expression; (3) biological metadata; (4) application of graphs and graph rendering; (5) machine learning for clustering and classification problems; (6) gene set enrichment analysis. Each chapter of this book describes an analysis of real data using hands-on example driven approaches. Short exercises help in the learning process and invite more advanced considerations of key topics. The book is a dynamic document. All the code shown can be executed on a local computer, and readers are able to reproduce every computation, figure, and table.
Book Synopsis Bioinformatics and Computational Biology Solutions Using R and Bioconductor by : Robert Gentleman
Download or read book Bioinformatics and Computational Biology Solutions Using R and Bioconductor written by Robert Gentleman and published by Springer Science & Business Media. This book was released on 2005-12-29 with total page 478 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Omic Association Studies with R and Bioconductor by : Juan R. González
Download or read book Omic Association Studies with R and Bioconductor written by Juan R. González and published by CRC Press. This book was released on 2019-06-14 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: After the great expansion of genome-wide association studies, their scientific methodology and, notably, their data analysis has matured in recent years, and they are a keystone in large epidemiological studies. Newcomers to the field are confronted with a wealth of data, resources and methods. This book presents current methods to perform informative analyses using real and illustrative data with established bioinformatics tools and guides the reader through the use of publicly available data. Includes clear, readable programming codes for readers to reproduce and adapt to their own data. Emphasises extracting biologically meaningful associations between traits of interest and genomic, transcriptomic and epigenomic data Uses up-to-date methods to exploit omic data Presents methods through specific examples and computing sessions Supplemented by a website, including code, datasets, and solutions
Book Synopsis Computer Simulation and Data Analysis in Molecular Biology and Biophysics by : Victor Bloomfield
Download or read book Computer Simulation and Data Analysis in Molecular Biology and Biophysics written by Victor Bloomfield and published by Springer Science & Business Media. This book was released on 2009-06-05 with total page 325 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an introduction to two important aspects of modern bioch- istry, molecular biology, and biophysics: computer simulation and data analysis. My aim is to introduce the tools that will enable students to learn and use some f- damental methods to construct quantitative models of biological mechanisms, both deterministicandwithsomeelementsofrandomness;tolearnhowconceptsofpr- ability can help to understand important features of DNA sequences; and to apply a useful set of statistical methods to analysis of experimental data. The availability of very capable but inexpensive personal computers and software makes it possible to do such work at a much higher level, but in a much easier way, than ever before. TheExecutiveSummaryofthein?uential2003reportfromtheNationalAcademy of Sciences, “BIO 2010: Transforming Undergraduate Education for Future - search Biologists” [12], begins The interplay of the recombinant DNA, instrumentation, and digital revolutions has p- foundly transformed biological research. The con?uence of these three innovations has led to important discoveries, such as the mapping of the human genome. How biologists design, perform, and analyze experiments is changing swiftly. Biological concepts and models are becoming more quantitative, and biological research has become critically dependent on concepts and methods drawn from other scienti?c disciplines. The connections between the biological sciences and the physical sciences, mathematics, and computer science are rapidly becoming deeper and more extensive.
Book Synopsis Microarray Technology in Practice by : Steve Russell
Download or read book Microarray Technology in Practice written by Steve Russell and published by Academic Press. This book was released on 2008-11-21 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt: Using chips composed of thousands of spots, each with the capability of holding DNA molecules corresponding to a given gene, DNA microarray technology has enabled researchers to measure simultaneously gene expression across the genome. As with other large-scale genomics approaches, microarray technologies are broadly applicable across disciplines of life and biomedical sciences, but remain daunting to many researchers. This guide is designed to demystify the technology and inform more biologists about this critically important experimental technique. - Cohesive overview of the technology and available platforms, followed by detailed discussion of experimental design and analysis of microarray experiments - Up-to-date description of normalization methods and current methods for sample amplification and labeling - Deep focus on oligonucleotide design, printing, labeling and hybridization, data acquisition, normalization, and meta-analysis - Additional uses of microarray technology such as ChIP (chromatin immunoprecipitation) with hybridization to DNA arrays, microarray-based comparative genomic hybridization (CGH), and cell and tissue arrays
Book Synopsis Statistical Bioinformatics by : Jae K. Lee
Download or read book Statistical Bioinformatics written by Jae K. Lee and published by John Wiley & Sons. This book was released on 2011-09-20 with total page 337 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Introduction to Computational Genomics by : Nello Cristianini
Download or read book Introduction to Computational Genomics written by Nello Cristianini and published by Cambridge University Press. This book was released on 2006-12-14 with total page 200 pages. Available in PDF, EPUB and Kindle. Book excerpt: Where did SARS come from? Have we inherited genes from Neanderthals? How do plants use their internal clock? The genomic revolution in biology enables us to answer such questions. But the revolution would have been impossible without the support of powerful computational and statistical methods that enable us to exploit genomic data. Many universities are introducing courses to train the next generation of bioinformaticians: biologists fluent in mathematics and computer science, and data analysts familiar with biology. This readable and entertaining book, based on successful taught courses, provides a roadmap to navigate entry to this field. It guides the reader through key achievements of bioinformatics, using a hands-on approach. Statistical sequence analysis, sequence alignment, hidden Markov models, gene and motif finding and more, are introduced in a rigorous yet accessible way. A companion website provides the reader with Matlab-related software tools for reproducing the steps demonstrated in the book.
Book Synopsis Microarray Gene Expression Data Analysis by : Helen Causton
Download or read book Microarray Gene Expression Data Analysis written by Helen Causton and published by John Wiley & Sons. This book was released on 2009-04-01 with total page 176 pages. Available in PDF, EPUB and Kindle. Book excerpt: This guide covers aspects of designing microarray experiments and analysing the data generated, including information on some of the tools that are available from non-commercial sources. Concepts and principles underpinning gene expression analysis are emphasised and wherever possible, the mathematics has been simplified. The guide is intended for use by graduates and researchers in bioinformatics and the life sciences and is also suitable for statisticians who are interested in the approaches currently used to study gene expression. Microarrays are an automated way of carrying out thousands of experiments at once, and allows scientists to obtain huge amounts of information very quickly Short, concise text on this difficult topic area Clear illustrations throughout Written by well-known teachers in the subject Provides insight into how to analyse the data produced from microarrays
Book Synopsis Gene Expression Studies Using Affymetrix Microarrays by : Hinrich Gohlmann
Download or read book Gene Expression Studies Using Affymetrix Microarrays written by Hinrich Gohlmann and published by CRC Press. This book was released on 2009-07-15 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Affymetrix GeneChip system is one of the most widely adapted microarray platforms. However, due to the overwhelming amount of information available, many Affymetrix users tend to stick to the default analysis settings and may end up drawing sub-optimal conclusions. Written by a molecular biologist and a biostatistician with a combined decade of
Book Synopsis Bacterial Genomics by : Aswin Sai Narain Seshasayee
Download or read book Bacterial Genomics written by Aswin Sai Narain Seshasayee and published by Cambridge University Press. This book was released on 2015-03-05 with total page 228 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of bacterial genetics has revolutionised with the development of genome sequencing, which let us catalogue the gene content of various clinically and industrially important bacteria and opened up the field of comparative genomics. The research findings on bacterial genetics were further enhanced by the development of allied techniques that allowed interrogation of the interactions and functions of the many components of the genome. These developments accelerated with the widespread adoption of quantitative deep-sequencing approaches. This process allowed both comparative and functional genomics on an unprecedented scale by presenting powerful tools to investigate multiple layers of bacterial adaptation and evolution. This book presents the application of genomic tools to examine bacterial adaptation. The emphasis is on data analysis and interpretation. Much of the material is drawn from the recent, primary literature, which is the most powerful tool in the cutting-edge and fast-growing field of bacterial research.
Download or read book Data Mining with R written by Luis Torgo and published by CRC Press. This book was released on 2016-11-30 with total page 426 pages. Available in PDF, EPUB and Kindle. Book excerpt: Data Mining with R: Learning with Case Studies, Second Edition uses practical examples to illustrate the power of R and data mining. Providing an extensive update to the best-selling first edition, this new edition is divided into two parts. The first part will feature introductory material, including a new chapter that provides an introduction to data mining, to complement the already existing introduction to R. The second part includes case studies, and the new edition strongly revises the R code of the case studies making it more up-to-date with recent packages that have emerged in R. The book does not assume any prior knowledge about R. Readers who are new to R and data mining should be able to follow the case studies, and they are designed to be self-contained so the reader can start anywhere in the document. The book is accompanied by a set of freely available R source files that can be obtained at the book’s web site. These files include all the code used in the case studies, and they facilitate the "do-it-yourself" approach followed in the book. Designed for users of data analysis tools, as well as researchers and developers, the book should be useful for anyone interested in entering the "world" of R and data mining. About the Author Luís Torgo is an associate professor in the Department of Computer Science at the University of Porto in Portugal. He teaches Data Mining in R in the NYU Stern School of Business’ MS in Business Analytics program. An active researcher in machine learning and data mining for more than 20 years, Dr. Torgo is also a researcher in the Laboratory of Artificial Intelligence and Data Analysis (LIAAD) of INESC Porto LA.
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.
Book Synopsis Behavioral Research Data Analysis with R by : Yuelin Li
Download or read book Behavioral Research Data Analysis with R written by Yuelin Li and published by Springer Science & Business Media. This book was released on 2011-12-02 with total page 247 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is written for behavioral scientists who want to consider adding R to their existing set of statistical tools, or want to switch to R as their main computation tool. The authors aim primarily to help practitioners of behavioral research make the transition to R. The focus is to provide practical advice on some of the widely-used statistical methods in behavioral research, using a set of notes and annotated examples. The book will also help beginners learn more about statistics and behavioral research. These are statistical techniques used by psychologists who do research on human subjects, but of course they are also relevant to researchers in others fields that do similar kinds of research. The authors emphasize practical data analytic skills so that they can be quickly incorporated into readers’ own research.
Book Synopsis Analysis of Integrated and Cointegrated Time Series with R by : Bernhard Pfaff
Download or read book Analysis of Integrated and Cointegrated Time Series with R written by Bernhard Pfaff and published by Springer Science & Business Media. This book was released on 2008-09-03 with total page 193 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is designed for self study. The reader can apply the theoretical concepts directly within R by following the examples.
Book Synopsis Statistical Analysis of Network Data with R by : Eric D. Kolaczyk
Download or read book Statistical Analysis of Network Data with R written by Eric D. Kolaczyk and published by Springer. This book was released on 2014-05-22 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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).
Book Synopsis Applied Spatial Data Analysis with R by : Roger S. Bivand
Download or read book Applied Spatial Data Analysis with R written by Roger S. Bivand and published by Springer Science & Business Media. This book was released on 2008-08-24 with total page 379 pages. Available in PDF, EPUB and Kindle. Book excerpt: We began writing this book in parallel with developing software for handling and analysing spatial data withR (R Development Core Team, 2008). - though the book is now complete, software development will continue, in the R community fashion, of rich and satisfying interaction with users around the world, of rapid releases to resolve problems, and of the usual joys and frust- tions of getting things done. There is little doubt that without pressure from users, the development ofR would not have reached its present scale, and the same applies to analysing spatial data analysis withR. It would, however, not be su?cient to describe the development of the R project mainly in terms of narrowly de?ned utility. In addition to being a communityprojectconcernedwiththedevelopmentofworld-classdataana- sis software implementations, it promotes speci?c choices with regard to how data analysis is carried out.R is open source not only because open source software development, including the dynamics of broad and inclusive user and developer communities, is arguably an attractive and successful development model.
Book Synopsis A User’s Guide to Network Analysis in R by : Douglas Luke
Download or read book A User’s Guide to Network Analysis in R written by Douglas Luke and published by Springer. This book was released on 2015-12-14 with total page 241 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presenting a comprehensive resource for the mastery of network analysis in R, the goal of Network Analysis with R is to introduce modern network analysis techniques in R to social, physical, and health scientists. The mathematical foundations of network analysis are emphasized in an accessible way and readers are guided through the basic steps of network studies: network conceptualization, data collection and management, network description, visualization, and building and testing statistical models of networks. As with all of the books in the Use R! series, each chapter contains extensive R code and detailed visualizations of datasets. Appendices will describe the R network packages and the datasets used in the book. An R package developed specifically for the book, available to readers on GitHub, contains relevant code and real-world network datasets as well.
