Bioconductor Case Studies

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Bioconductor Case Studies

Florian Hahne,Wolfgang Huber,Robert Gentleman,Seth Falcon
Bioconductor Case Studies Book PDF

Author : Florian Hahne,Wolfgang Huber,Robert Gentleman,Seth Falcon
Publisher : Springer Science & Business Media
Page : 284 pages
File Size : 42,6 Mb
Release : 2010-06-09
Category : Science
ISBN : 9780387772400

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Bioconductor Case Studies by Florian Hahne,Wolfgang Huber,Robert Gentleman,Seth Falcon Pdf

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.

Bioinformatics and Computational Biology Solutions Using R and Bioconductor

Robert Gentleman,Vincent Carey,Wolfgang Huber,Rafael Irizarry,Sandrine Dudoit
Bioinformatics and Computational Biology Solutions Using R and Bioconductor Book PDF

Author : Robert Gentleman,Vincent Carey,Wolfgang Huber,Rafael Irizarry,Sandrine Dudoit
Publisher : Springer Science & Business Media
Page : 478 pages
File Size : 46,5 Mb
Release : 2005-12-29
Category : Computers
ISBN : 9780387293622

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Bioinformatics and Computational Biology Solutions Using R and Bioconductor by Robert Gentleman,Vincent Carey,Wolfgang Huber,Rafael Irizarry,Sandrine Dudoit Pdf

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.

Omic Association Studies with R and Bioconductor

Juan R. González,Alejandro Cáceres
Omic Association Studies with R and Bioconductor Book PDF

Author : Juan R. González,Alejandro Cáceres
Publisher : CRC Press
Page : 348 pages
File Size : 46,6 Mb
Release : 2019-06-14
Category : Mathematics
ISBN : 9780429803369

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Omic Association Studies with R and Bioconductor by Juan R. González,Alejandro Cáceres Pdf

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

Computer Simulation and Data Analysis in Molecular Biology and Biophysics

Victor Bloomfield
Computer Simulation and Data Analysis in Molecular Biology and Biophysics Book PDF

Author : Victor Bloomfield
Publisher : Springer Science & Business Media
Page : 325 pages
File Size : 40,6 Mb
Release : 2009-06-05
Category : Science
ISBN : 9781441900838

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Computer Simulation and Data Analysis in Molecular Biology and Biophysics by Victor Bloomfield Pdf

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.

Gene Expression Studies Using Affymetrix Microarrays

Hinrich Gohlmann,Willem Talloen
Gene Expression Studies Using Affymetrix Microarrays Book PDF

Author : Hinrich Gohlmann,Willem Talloen
Publisher : CRC Press
Page : 359 pages
File Size : 41,7 Mb
Release : 2009-07-15
Category : Science
ISBN : 1420065165

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Gene Expression Studies Using Affymetrix Microarrays by Hinrich Gohlmann,Willem Talloen Pdf

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 experience in practical expression profiling experiments and data analyses, Gene Expression Studies Using Affymetrix Microarrays tears down the omnipresent language barriers among molecular biology, bioinformatics, and biostatistics by explaining the entire process of a gene expression study from conception to conclusion. Truly Multidisciplinary: Merges Molecular Biology, Bioinformatics, and Biostatistics This authoritative resource covers important technical and statistical pitfalls and problems, helping not only to explain concepts outside the domain of researchers, but to provide additional guidance in their field of expertise. The book also describes technical and statistical methods conceptually with illustrative, full-color examples, enabling those inexperienced with gene expression studies to grasp the basic principles. Gene Expression Studies Using Affymetrix Microarrays provides novices with a detailed, yet focused introductory course and practical user guide. Specialized experts will also find it useful as a translation dictionary to understand other involved disciplines or to get a broader picture of microarray gene expression studies in general. Although focusing on Affymetrix gene expression, this globally relevant guide covers topics that are equally useful for other microarray platforms and other Affymetrix applications.

Bacterial Genomics

Aswin Sai Narain Seshasayee
Bacterial Genomics Book PDF

Author : Aswin Sai Narain Seshasayee
Publisher : Cambridge University Press
Page : 227 pages
File Size : 44,9 Mb
Release : 2015-03-05
Category : Science
ISBN : 9781107079830

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Bacterial Genomics by Aswin Sai Narain Seshasayee Pdf

This book presents the application of genomic tools to examine bacterial adaptation. The emphasis is on data analysis and interpretation.

Statistical Bioinformatics

Jae K. Lee
Statistical Bioinformatics Book PDF

Author : Jae K. Lee
Publisher : John Wiley & Sons
Page : 337 pages
File Size : 45,7 Mb
Release : 2011-09-20
Category : Medical
ISBN : 9781118211526

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Statistical Bioinformatics by Jae K. Lee Pdf

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.

Microarray Technology in Practice

Steve Russell,Lisa A. Meadows,Roslin R. Russell
Microarray Technology in Practice Book PDF

Author : Steve Russell,Lisa A. Meadows,Roslin R. Russell
Publisher : Academic Press
Page : 464 pages
File Size : 41,7 Mb
Release : 2008-11-21
Category : Science
ISBN : 0080919766

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Microarray Technology in Practice by Steve Russell,Lisa A. Meadows,Roslin R. Russell Pdf

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

Data Mining with R

Luis Torgo
Data Mining with R Book PDF

Author : Luis Torgo
Publisher : CRC Press
Page : 426 pages
File Size : 49,9 Mb
Release : 2016-11-30
Category : Business & Economics
ISBN : 9781315399096

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Data Mining with R by Luis Torgo Pdf

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.

Medical Statistics for Cancer Studies

Trevor F. Cox
Medical Statistics for Cancer Studies Book PDF

Author : Trevor F. Cox
Publisher : CRC Press
Page : 334 pages
File Size : 55,6 Mb
Release : 2022-06-23
Category : Mathematics
ISBN : 9781000601107

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Medical Statistics for Cancer Studies by Trevor F. Cox Pdf

Cancer is a dreaded disease. One in two people will be diagnosed with cancer within their lifetime. Medical Statistics for Cancer Studies shows how cancer data can be analysed in a variety of ways, covering cancer clinical trial data, epidemiological data, biological data, and genetic data. It gives some background in cancer biology and genetics, followed by detailed overviews of survival analysis, clinical trials, regression analysis, epidemiology, meta-analysis, biomarkers, and cancer informatics. It includes lots of examples using real data from the author’s many years of experience working in a cancer clinical trials unit. Features: A broad and accessible overview of statistical methods in cancer research Necessary background in cancer biology and genetics Details of statistical methodology with minimal algebra Many examples using real data from cancer clinical trials Appendix giving statistics revision.

Primer to Analysis of Genomic Data Using R

Cedric Gondro
Primer to Analysis of Genomic Data Using R Book PDF

Author : Cedric Gondro
Publisher : Springer
Page : 270 pages
File Size : 53,5 Mb
Release : 2015-05-18
Category : Medical
ISBN : 9783319144757

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Primer to Analysis of Genomic Data Using R by Cedric Gondro Pdf

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.

Computational Science – ICCS 2009

Gabrielle Allen,Jaroslaw Nabrzyski,Edward Seidel,Geert Dick van Albada,Jack Dongarra,Peter M.A. Sloot
Computational Science ICCS 2009 Book PDF

Author : Gabrielle Allen,Jaroslaw Nabrzyski,Edward Seidel,Geert Dick van Albada,Jack Dongarra,Peter M.A. Sloot
Publisher : Springer Science & Business Media
Page : 940 pages
File Size : 51,9 Mb
Release : 2009-05-19
Category : Computers
ISBN : 9783642019722

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Computational Science – ICCS 2009 by Gabrielle Allen,Jaroslaw Nabrzyski,Edward Seidel,Geert Dick van Albada,Jack Dongarra,Peter M.A. Sloot Pdf

The two-volume set LNCS 5544-5545 constitutes the refereed proceedings of the 9th International Conference on Computational Science, ICCS 2009, held in Baton Rouge, LA, USA in May 2008. The 60 revised papers of the main conference track presented together with the abstracts of 5 keynote talks and the 138 revised papers from 13 workshops were carefully reviewed and selected for inclusion in the three volumes. The general main track of ICSS 2009 was organized in about 20 parallel sessions addressing the following topics: e-Science Applications and Systems, Scheduling, Software Services and Tools, New Hardware and Its Applications, Computer Networks, Simulation of Complex Systems, Image Processing, Optimization Techniques, and Numerical Methods.

R in a Nutshell

Joseph Adler
R in a Nutshell Book PDF

Author : Joseph Adler
Publisher : "O'Reilly Media, Inc."
Page : 723 pages
File Size : 43,7 Mb
Release : 2012-10-09
Category : Computers
ISBN : 9781449312084

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R in a Nutshell by Joseph Adler Pdf

Presents a guide to the R computer language, covering such topics as the user interface, packages, syntax, objects, functions, object-oriented programming, data sets, lattice graphics, regression models, and bioconductor.

Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R

Gabriel Valiente
Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R Book PDF

Author : Gabriel Valiente
Publisher : CRC Press
Page : 368 pages
File Size : 42,7 Mb
Release : 2009-04-08
Category : Science
ISBN : 1420069748

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Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R by Gabriel Valiente Pdf

Emphasizing the search for patterns within and between biological sequences, trees, and graphs, Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R shows how combinatorial pattern matching algorithms can solve computational biology problems that arise in the analysis of genomic, transcriptomic, proteomic, metabolomic, and interactomic data. It implements the algorithms in Perl and R, two widely used scripting languages in computational biology. The book provides a well-rounded explanation of traditional issues as well as an up-to-date account of more recent developments, such as graph similarity and search. It is organized around the specific algorithmic problems that arise when dealing with structures that are commonly found in computational biology, including biological sequences, trees, and graphs. For each of these structures, the author makes a clear distinction between problems that arise in the analysis of one structure and in the comparative analysis of two or more structures. He also presents phylogenetic trees and networks as examples of trees and graphs in computational biology. This book supplies a comprehensive view of the whole field of combinatorial pattern matching from a computational biology perspective. Along with thorough discussions of each biological problem, it includes detailed algorithmic solutions in pseudo-code, full Perl and R implementation, and pointers to other software, such as those on CPAN and CRAN.

Bioinformatics and Computational Biology

Basant K. Tiwary
Bioinformatics and Computational Biology Book PDF

Author : Basant K. Tiwary
Publisher : Springer Nature
Page : 239 pages
File Size : 55,6 Mb
Release : 2021-11-23
Category : Medical
ISBN : 9789811642418

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Bioinformatics and Computational Biology by Basant K. Tiwary Pdf

This textbook introduces fundamental concepts of bioinformatics and computational biology to the students and researchers in biology, medicine, veterinary science, agriculture, and bioengineering . The respective chapters provide detailed information on biological databases, sequence alignment, molecular evolution, next-generation sequencing, systems biology, and statistical computing using R. The book also presents a case-based discussion on clinical, veterinary, agricultural bioinformatics, and computational bioengineering for application-based learning in the respective fields. Further, it offers readers guidance on reconstructing and analysing biological networks and highlights computational methods used in systems medicine and genome-wide association mapping of diseases. Given its scope, this textbook offers an essential introductory book on bioinformatics and computational biology for undergraduate and graduate students in the life sciences, botany, zoology, physiology, biotechnology, bioinformatics, and genomic science as well as systems biology, bioengineering and the agricultural, and veterinary sciences.