Statistics And Data Analysis For Microarrays Using R And Bioconductor Second Edition

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Statistics and Data Analysis for Microarrays Using R and Bioconductor

Author : Sorin Draghici
Publisher : CRC Press
ISBN 13 : 1439809763
Total Pages : 1076 pages
Book Rating : 4.4/5 (398 download)

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Book Synopsis Statistics and Data Analysis for Microarrays Using R and Bioconductor by : Sorin Draghici

Download or read book Statistics and Data Analysis for Microarrays Using R and Bioconductor written by Sorin Draghici and published by CRC Press. This book was released on 2016-04-19 with total page 1076 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Bioinformatics and Computational Biology Solutions Using R and Bioconductor

Author : Robert Gentleman
Publisher : Springer Science & Business Media
ISBN 13 : 0387293620
Total Pages : 478 pages
Book Rating : 4.3/5 (872 download)

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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.

Microarray Image and Data Analysis

Author : Luis Rueda
Publisher : CRC Press
ISBN 13 : 1466586877
Total Pages : 516 pages
Book Rating : 4.4/5 (665 download)

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Book Synopsis Microarray Image and Data Analysis by : Luis Rueda

Download or read book Microarray Image and Data Analysis written by Luis Rueda and published by CRC Press. This book was released on 2018-09-03 with total page 516 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microarray Image and Data Analysis: Theory and Practice is a compilation of the latest and greatest microarray image and data analysis methods from the multidisciplinary international research community. Delivering a detailed discussion of the biological aspects and applications of microarrays, the book: Describes the key stages of image processing, gridding, segmentation, compression, quantification, and normalization Features cutting-edge approaches to clustering, biclustering, and the reconstruction of regulatory networks Covers different types of microarrays such as DNA, protein, tissue, and low- and high-density oligonucleotide arrays Examines the current state of various microarray technologies, including their availability and affordability Explains how data generated by microarray experiments are analyzed to obtain meaningful biological conclusions An essential reference for academia and industry, Microarray Image and Data Analysis: Theory and Practice provides readers with valuable tools and techniques that extend to a wide range of biological studies and microarray platforms.

Data Analysis for the Life Sciences with R

Author : Rafael A. Irizarry
Publisher : CRC Press
ISBN 13 : 1498775861
Total Pages : 537 pages
Book Rating : 4.4/5 (987 download)

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Book Synopsis Data Analysis for the Life Sciences with R by : Rafael A. Irizarry

Download or read book Data Analysis for the Life Sciences with R written by Rafael A. Irizarry and published by CRC Press. This book was released on 2016-10-04 with total page 537 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Big Data Analysis for Bioinformatics and Biomedical Discoveries

Author : Shui Qing Ye
Publisher : CRC Press
ISBN 13 : 149872454X
Total Pages : 286 pages
Book Rating : 4.4/5 (987 download)

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Book Synopsis Big Data Analysis for Bioinformatics and Biomedical Discoveries by : Shui Qing Ye

Download or read book Big Data Analysis for Bioinformatics and Biomedical Discoveries written by Shui Qing Ye and published by CRC Press. This book was released on 2016-01-13 with total page 286 pages. Available in PDF, EPUB and Kindle. Book excerpt: Demystifies Biomedical and Biological Big Data AnalysesBig Data Analysis for Bioinformatics and Biomedical Discoveries provides a practical guide to the nuts and bolts of Big Data, enabling you to quickly and effectively harness the power of Big Data to make groundbreaking biological discoveries, carry out translational medical research, and implem

RNA-seq Data Analysis

Author : Eija Korpelainen
Publisher : CRC Press
ISBN 13 : 1466595019
Total Pages : 314 pages
Book Rating : 4.4/5 (665 download)

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Book Synopsis RNA-seq Data Analysis by : Eija Korpelainen

Download or read book RNA-seq Data Analysis written by Eija Korpelainen and published by CRC Press. This book was released on 2014-09-19 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: The State of the Art in Transcriptome AnalysisRNA sequencing (RNA-seq) data offers unprecedented information about the transcriptome, but harnessing this information with bioinformatics tools is typically a bottleneck. RNA-seq Data Analysis: A Practical Approach enables researchers to examine differential expression at gene, exon, and transcript le

Statistical and Computational Methods in Brain Image Analysis

Author : Moo K. Chung
Publisher : CRC Press
ISBN 13 : 1439836612
Total Pages : 465 pages
Book Rating : 4.4/5 (398 download)

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Book Synopsis Statistical and Computational Methods in Brain Image Analysis by : Moo K. Chung

Download or read book Statistical and Computational Methods in Brain Image Analysis written by Moo K. Chung and published by CRC Press. This book was released on 2013-07-23 with total page 465 pages. Available in PDF, EPUB and Kindle. Book excerpt: The massive amount of nonstandard high-dimensional brain imaging data being generated is often difficult to analyze using current techniques. This challenge in brain image analysis requires new computational approaches and solutions. But none of the research papers or books in the field describe the quantitative techniques with detailed illustrations of actual imaging data and computer codes. Using MATLAB® and case study data sets, Statistical and Computational Methods in Brain Image Analysis is the first book to explicitly explain how to perform statistical analysis on brain imaging data. The book focuses on methodological issues in analyzing structural brain imaging modalities such as MRI and DTI. Real imaging applications and examples elucidate the concepts and methods. In addition, most of the brain imaging data sets and MATLAB codes are available on the author’s website. By supplying the data and codes, this book enables researchers to start their statistical analyses immediately. Also suitable for graduate students, it provides an understanding of the various statistical and computational methodologies used in the field as well as important and technically challenging topics.

Big Data in Omics and Imaging

Author : Momiao Xiong
Publisher : CRC Press
ISBN 13 : 1498725805
Total Pages : 668 pages
Book Rating : 4.4/5 (987 download)

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Book Synopsis Big Data in Omics and Imaging by : Momiao Xiong

Download or read book Big Data in Omics and Imaging written by Momiao Xiong and published by CRC Press. This book was released on 2017-12-01 with total page 668 pages. Available in PDF, EPUB and Kindle. Book excerpt: Big Data in Omics and Imaging: Association Analysis addresses the recent development of association analysis and machine learning for both population and family genomic data in sequencing era. It is unique in that it presents both hypothesis testing and a data mining approach to holistically dissecting the genetic structure of complex traits and to designing efficient strategies for precision medicine. The general frameworks for association analysis and machine learning, developed in the text, can be applied to genomic, epigenomic and imaging data. FEATURES Bridges the gap between the traditional statistical methods and computational tools for small genetic and epigenetic data analysis and the modern advanced statistical methods for big data Provides tools for high dimensional data reduction Discusses searching algorithms for model and variable selection including randomization algorithms, Proximal methods and matrix subset selection Provides real-world examples and case studies Will have an accompanying website with R code The book is designed for graduate students and researchers in genomics, bioinformatics, and data science. It represents the paradigm shift of genetic studies of complex diseases– from shallow to deep genomic analysis, from low-dimensional to high dimensional, multivariate to functional data analysis with next-generation sequencing (NGS) data, and from homogeneous populations to heterogeneous population and pedigree data analysis. Topics covered are: advanced matrix theory, convex optimization algorithms, generalized low rank models, functional data analysis techniques, deep learning principle and machine learning methods for modern association, interaction, pathway and network analysis of rare and common variants, biomarker identification, disease risk and drug response prediction.

Computational Exome and Genome Analysis

Author : Peter N. Robinson
Publisher : CRC Press
ISBN 13 : 1498775993
Total Pages : 575 pages
Book Rating : 4.4/5 (987 download)

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Book Synopsis Computational Exome and Genome Analysis by : Peter N. Robinson

Download or read book Computational Exome and Genome Analysis written by Peter N. Robinson and published by CRC Press. This book was released on 2017-09-13 with total page 575 pages. Available in PDF, EPUB and Kindle. Book excerpt: Exome and genome sequencing are revolutionizing medical research and diagnostics, but the computational analysis of the data has become an extremely heterogeneous and often challenging area of bioinformatics. Computational Exome and Genome Analysis provides a practical introduction to all of the major areas in the field, enabling readers to develop a comprehensive understanding of the sequencing process and the entire computational analysis pipeline.

Molecular Data Analysis Using R

Author : Csaba Ortutay
Publisher : John Wiley & Sons
ISBN 13 : 1119165024
Total Pages : 354 pages
Book Rating : 4.1/5 (191 download)

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Book Synopsis Molecular Data Analysis Using R by : Csaba Ortutay

Download or read book Molecular Data Analysis Using R written by Csaba Ortutay and published by John Wiley & Sons. This book was released on 2017-02-06 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 Modeling and Machine Learning for Molecular Biology

Author : Alan Moses
Publisher : CRC Press
ISBN 13 : 1482258609
Total Pages : 281 pages
Book Rating : 4.4/5 (822 download)

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Book Synopsis Statistical Modeling and Machine Learning for Molecular Biology by : Alan Moses

Download or read book Statistical Modeling and Machine Learning for Molecular Biology written by Alan Moses and published by CRC Press. This book was released on 2017-01-06 with total page 281 pages. Available in PDF, EPUB and Kindle. Book excerpt: • Assumes no background in statistics or computers • Covers most major types of molecular biological data • Covers the statistical and machine learning concepts of most practical utility (P-values, clustering, regression, regularization and classification) • Intended for graduate students beginning careers in molecular biology, systems biology, bioengineering and genetics

Mathematical Models of Plant-Herbivore Interactions

Author : Zhilan Feng
Publisher : CRC Press
ISBN 13 : 1498769187
Total Pages : 240 pages
Book Rating : 4.4/5 (987 download)

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Book Synopsis Mathematical Models of Plant-Herbivore Interactions by : Zhilan Feng

Download or read book Mathematical Models of Plant-Herbivore Interactions written by Zhilan Feng and published by CRC Press. This book was released on 2017-09-07 with total page 240 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mathematical Models of Plant-Herbivore Interactions addresses mathematical models in the study of practical questions in ecology, particularly factors that affect herbivory, including plant defense, herbivore natural enemies, and adaptive herbivory, as well as the effects of these on plant community dynamics. The result of extensive research on the use of mathematical modeling to investigate the effects of plant defenses on plant-herbivore dynamics, this book describes a toxin-determined functional response model (TDFRM) that helps explains field observations of these interactions. This book is intended for graduate students and researchers interested in mathematical biology and ecology.

Stochastic Modelling for Systems Biology, Second Edition

Author : Darren J. Wilkinson
Publisher : CRC Press
ISBN 13 : 1439837724
Total Pages : 365 pages
Book Rating : 4.4/5 (398 download)

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Book Synopsis Stochastic Modelling for Systems Biology, Second Edition by : Darren J. Wilkinson

Download or read book Stochastic Modelling for Systems Biology, Second Edition written by Darren J. Wilkinson and published by CRC Press. This book was released on 2011-11-09 with total page 365 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the first edition of Stochastic Modelling for Systems Biology, there have been many interesting developments in the use of "likelihood-free" methods of Bayesian inference for complex stochastic models. Re-written to reflect this modern perspective, this second edition covers everything necessary for a good appreciation of stochastic kinetic modelling of biological networks in the systems biology context. Keeping with the spirit of the first edition, all of the new theory is presented in a very informal and intuitive manner, keeping the text as accessible as possible to the widest possible readership. New in the Second Edition All examples have been updated to Systems Biology Markup Language Level 3 All code relating to simulation, analysis, and inference for stochastic kinetic models has been re-written and re-structured in a more modular way An ancillary website provides links, resources, errata, and up-to-date information on installation and use of the associated R package More background material on the theory of Markov processes and stochastic differential equations, providing more substance for mathematically inclined readers Discussion of some of the more advanced concepts relating to stochastic kinetic models, such as random time change representations, Kolmogorov equations, Fokker-Planck equations and the linear noise approximation Simple modelling of "extrinsic" and "intrinsic" noise An effective introduction to the area of stochastic modelling in computational systems biology, this new edition adds additional mathematical detail and computational methods that will provide a stronger foundation for the development of more advanced courses in stochastic biological modelling.

Computational and Visualization Techniques for Structural Bioinformatics Using Chimera

Author : Forbes J. Burkowski
Publisher : CRC Press
ISBN 13 : 1439836620
Total Pages : 453 pages
Book Rating : 4.4/5 (398 download)

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Book Synopsis Computational and Visualization Techniques for Structural Bioinformatics Using Chimera by : Forbes J. Burkowski

Download or read book Computational and Visualization Techniques for Structural Bioinformatics Using Chimera written by Forbes J. Burkowski and published by CRC Press. This book was released on 2014-07-29 with total page 453 pages. Available in PDF, EPUB and Kindle. Book excerpt: A Step-by-Step Guide to Describing Biomolecular StructureComputational and Visualization Techniques for Structural Bioinformatics Using Chimera shows how to perform computations with Python scripts in the Chimera environment. It focuses on the three core areas needed to study structural bioinformatics: biochemistry, mathematics, and computation.Und

Introduction to Proteins

Author : Amit Kessel
Publisher : CRC Press
ISBN 13 : 1498747213
Total Pages : 1423 pages
Book Rating : 4.4/5 (987 download)

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Book Synopsis Introduction to Proteins by : Amit Kessel

Download or read book Introduction to Proteins written by Amit Kessel and published by CRC Press. This book was released on 2018-03-22 with total page 1423 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introduction to Proteins provides a comprehensive and state-of-the-art introduction to the structure, function, and motion of proteins for students, faculty, and researchers at all levels. The book covers proteins and enzymes across a wide range of contexts and applications, including medical disorders, drugs, toxins, chemical warfare, and animal behavior. Each chapter includes a Summary, Exercies, and References. New features in the thoroughly-updated second edition include: A brand-new chapter on enzymatic catalysis, describing enzyme biochemistry, classification, kinetics, thermodynamics, mechanisms, and applications in medicine and other industries. These are accompanied by multiple animations of biochemical reactions and mechanisms, accessible via embedded QR codes (which can be viewed by smartphones) An in-depth discussion of G-protein-coupled receptors (GPCRs) A wider-scale description of biochemical and biophysical methods for studying proteins, including fully accessible internet-based resources, such as databases and algorithms Animations of protein dynamics and conformational changes, accessible via embedded QR codes Additional features Extensive discussion of the energetics of protein folding, stability and interactions A comprehensive view of membrane proteins, with emphasis on structure-function relationship Coverage of intrinsically unstructured proteins, providing a complete, realistic view of the proteome and its underlying functions Exploration of industrial applications of protein engineering and rational drug design Each chapter includes a Summary, Exercies, and References Approximately 300 color images Downloadable solutions manual available at www.crcpress.com For more information, including all presentations, tables, animations, and exercises, as well as a complete teaching course on proteins' structure and function, please visit the author's website: http://ibis.tau.ac.il/wiki/nir_bental/index.php/Introduction_to_Proteins_Book. Praise for the first edition "This book captures, in a very accessible way, a growing body of literature on the structure, function and motion of proteins. This is a superb publication that would be very useful to undergraduates, graduate students, postdoctoral researchers, and instructors involved in structural biology or biophysics courses or in research on protein structure-function relationships." --David Sheehan, ChemBioChem, 2011 "Introduction to Proteins is an excellent, state-of-the-art choice for students, faculty, or researchers needing a monograph on protein structure. This is an immensely informative, thoroughly researched, up-to-date text, with broad coverage and remarkable depth. Introduction to Proteins would provide an excellent basis for an upper-level or graduate course on protein structure, and a valuable addition to the libraries of professionals interested in this centrally important field." --Eric Martz, Biochemistry and Molecular Biology Education, 2012

An Introduction to Physical Oncology

Author : Vittorio Cristini
Publisher : CRC Press
ISBN 13 : 1466551364
Total Pages : 204 pages
Book Rating : 4.4/5 (665 download)

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Book Synopsis An Introduction to Physical Oncology by : Vittorio Cristini

Download or read book An Introduction to Physical Oncology written by Vittorio Cristini and published by CRC Press. This book was released on 2017-06-26 with total page 204 pages. Available in PDF, EPUB and Kindle. Book excerpt: Physical oncology has the potential to revolutionize cancer research and treatment. The fundamental rationale behind this approach is that physical processes, such as transport mechanisms for drug molecules within tissue and forces exchanged by cancer cells with tissue, may play an equally important role as biological processes in influencing progression and treatment outcome. This book introduces the emerging field of physical oncology to a general audience, with a focus on recent breakthroughs that help in the design and discovery of more effective cancer treatments. It describes how novel mathematical models of physical transport processes incorporate patient tissue and imaging data routinely produced in the clinic to predict the efficacy of many cancer treatment approaches, including chemotherapy and radiation therapy. By helping to identify which therapies would be most beneficial for an individual patient, and quantifying their effects prior to actual implementation in the clinic, physical oncology allows doctors to design treatment regimens customized to each patient’s clinical needs, significantly altering the current clinical approach to cancer treatment and improving the outcomes for patients.

Python for Bioinformatics

Author : Sebastian Bassi
Publisher : CRC Press
ISBN 13 : 1351976958
Total Pages : 423 pages
Book Rating : 4.3/5 (519 download)

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Book Synopsis Python for Bioinformatics by : Sebastian Bassi

Download or read book Python for Bioinformatics written by Sebastian Bassi and published by CRC Press. This book was released on 2017-08-07 with total page 423 pages. Available in PDF, EPUB and Kindle. Book excerpt: In today's data driven biology, programming knowledge is essential in turning ideas into testable hypothesis. Based on the author’s extensive experience, Python for Bioinformatics, Second Edition helps biologists get to grips with the basics of software development. Requiring no prior knowledge of programming-related concepts, the book focuses on the easy-to-use, yet powerful, Python computer language. This new edition is updated throughout to Python 3 and is designed not just to help scientists master the basics, but to do more in less time and in a reproducible way. New developments added in this edition include NoSQL databases, the Anaconda Python distribution, graphical libraries like Bokeh, and the use of Github for collaborative development.