Bioconductor Case Studies
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Bioconductor Case Studies
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Author : Florian Hahne
language : en
Publisher: Springer Science & Business Media
Release Date : 2010-06-09
Bioconductor Case Studies written by Florian Hahne and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-06-09 with Science categories.
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
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Author : Robert Gentleman
language : en
Publisher: Springer Science & Business Media
Release Date : 2005-12-29
Bioinformatics And Computational Biology Solutions Using R And Bioconductor written by Robert Gentleman and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005-12-29 with Computers categories.
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.
Computer Simulation And Data Analysis In Molecular Biology And Biophysics
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Author : Victor Bloomfield
language : en
Publisher: Springer Science & Business Media
Release Date : 2009-06-05
Computer Simulation And Data Analysis In Molecular Biology And Biophysics written by Victor Bloomfield and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-06-05 with Science categories.
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.
Exploring Bioinformatics
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Author : Caroline St. Clair
language : en
Publisher: Jones & Bartlett Publishers
Release Date : 2013-12-12
Exploring Bioinformatics written by Caroline St. Clair and has been published by Jones & Bartlett Publishers this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-12-12 with Computers categories.
Thoroughly revised and updated, Exploring Bioinformatics: A Project-Based Approach, Second Edition is intended for an introductory course in bioinformatics at the undergraduate level. Through hands-on projects, students are introduced to current biological problems and then explore and develop bioinformatic solutions to these issues. Each chapter presents a key problem, provides basic biological concepts, introduces computational techniques to address the problem, and guides students through the use of existing web-based tools and software solutions. This progression prepares students to tackle the On-Your-Own Project, where they develop their own software solutions. Topics such as antibiotic resistance, genetic disease, and genome sequencing provide context and relevance to capture student interest.
Computational Genomics With R
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Author : Altuna Akalin
language : en
Publisher: CRC Press
Release Date : 2020-12-16
Computational Genomics With R written by Altuna Akalin and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-12-16 with Mathematics categories.
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.
Machine Learning An Overview With The Help Of R Software
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Author : Editor IJSMI
language : en
Publisher: IJSMI
Release Date : 2018-11-21
Machine Learning An Overview With The Help Of R Software written by Editor IJSMI and has been published by IJSMI this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-11-21 with Computers categories.
This book intends to provide an overview of Machine Learning and its algorithms & models with help of R software. Machine learning forms the basis for Artificial Intelligence which will play a crucial role in day to day life of human beings in the near future. A basic understanding of machine learning is required, as its application is widely seen in different fields such as banks and financial sectors, manufacturing, aviation, transportation and medical field. The book covers machine learning classification algorithms such as K-Nearest Neighborhood, Naïve Bayes, Decision Trees and also Artificial Neural Networks and Support Vector Machines. It is recommended to refer author’s book on Application of Statistical Tools in Biomedical Domain: An Overview with Help of Software (https://www.amazon.com/dp/1986988554) and Essentials of Bio-Statistics: An overview with the help of Software https://www.amazon.com/dp/B07GRBXX7D if you need to familiarize yourself with the basic statistical knowledge. Editor International Journal of Statistics and Medical Informatics www.ijsmi.com/book.php Amazon link https://www.amazon.com/dp/1790122627 (Paper Back) https://www.amazon.com/dp/B07KQSN447 (Kindle Edition)
Numerical Ecology With R
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Author : Daniel Borcard
language : en
Publisher: Springer Science & Business Media
Release Date : 2011-01-07
Numerical Ecology With R written by Daniel Borcard and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-01-07 with Medical categories.
Numerical Ecology with R provides a long-awaited bridge between a textbook in Numerical Ecology and the implementation of this discipline in the R language. After short theoretical overviews, the authors accompany the users through the exploration of the methods by means of applied and extensively commented examples. Users are invited to use this book as a teaching companion at the computer. The travel starts with exploratory approaches, proceeds with the construction of association matrices, then addresses three families of methods: clustering, unconstrained and canonical ordination, and spatial analysis. All the necessary data files, the scripts used in the chapters, as well as the extra R functions and packages written by the authors, can be downloaded from a web page accessible through the Springer web site(http://adn.biol.umontreal.ca/~numericalecology/numecolR/). This book is aimed at professional researchers, practitioners, graduate students and teachers in ecology, environmental science and engineering, and in related fields such as oceanography, molecular ecology, agriculture and soil science, who already have a background in general and multivariate statistics and wish to apply this knowledge to their data using the R language, as well as people willing to accompany their disciplinary learning with practical applications. People from other fields (e.g. geology, geography, paleoecology, phylogenetics, anthropology, the social and education sciences, etc.) may also benefit from the materials presented in this book. The three authors teach numerical ecology, both theoretical and practical, to a wide array of audiences, in regular courses in their Universities and in short courses given around the world. Daniel Borcard is lecturer of Biostatistics and Ecology and researcher in Numerical Ecology at Université de Montréal, Québec, Canada. François Gillet is professor of Community Ecology and Ecological Modelling at Université de Franche-Comté, Besançon, France. Pierre Legendre is professor of Quantitative Biology and Ecology at Université de Montréal, Fellow of the Royal Society of Canada, and ISI Highly Cited Researcher in Ecology/Environment.
Clinical Trial Data Analysis Using R
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Author : Ding-Geng (Din) Chen
language : en
Publisher: CRC Press
Release Date : 2010-12-14
Clinical Trial Data Analysis Using R written by Ding-Geng (Din) Chen and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-12-14 with Mathematics categories.
Too often in biostatistical research and clinical trials, a knowledge gap exists between developed statistical methods and the applications of these methods. Filling this gap, Clinical Trial Data Analysis Using R provides a thorough presentation of biostatistical analyses of clinical trial data and shows step by step how to implement the statistical methods using R. The book’s practical, detailed approach draws on the authors’ 30 years of real-world experience in biostatistical research and clinical development. Each chapter presents examples of clinical trials based on the authors’ actual experiences in clinical drug development. Various biostatistical methods for analyzing the data are then identified. The authors develop analysis code step by step using appropriate R packages and functions. This approach enables readers to gain an understanding of the analysis methods and R implementation so that they can use R to analyze their own clinical trial data. With step-by-step illustrations of R implementations, this book shows how to easily use R to simulate and analyze data from a clinical trial. It describes numerous up-to-date statistical methods and offers sound guidance on the processes involved in clinical trials.
Morphometrics With R
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Author : Julien Claude
language : en
Publisher: Springer Science & Business Media
Release Date : 2008-12-15
Morphometrics With R written by Julien Claude and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-12-15 with Science categories.
This book aims to explain how to use R to perform morphometrics. Morpho- tric analysis is the study of shape and size variations and covariations and their covariations with other variables. Morphometrics is thus deeply rooted within stat- tical sciences. While most applications concern biology, morphometrics is becoming common tools used in archeological, palaeontological, geographical, or medicine disciplines. Since the recent formalizations of some of the ideas of predecessors, such as D’arcy Thompson, and thanks to the development of computer techno- gies and new ways for appraising shape changes and variation, morphometrics have undergone, and are still undergoing, a revolution. Most techniques dealing with s- tistical shape analysis have been developed in the last three decades, and the number of publications using morphometrics is increasing rapidly. However, the majority of these methods cannot be implemented in available software and therefore prosp- tive students often need to acquire detailed knowledge in informatics and statistics before applying them to their data. With acceleration in the accumulation of me- ods accompanying the emerging science of statistical shape analysis, it is becoming important to use tools that allow some autonomy. R easily helps ful?ll this need. Risalanguage andenvironment forstatisticalcomputingandgraphics. Although there is an increasing number of computer applications that perform morphometrics, using R has several advantages that confer to users considerable power and possible new horizons in a world that requires rapid adaptability.
The International Conference On Advanced Machine Learning Technologies And Applications Amlta2019
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Author : Aboul Ella Hassanien
language : en
Publisher: Springer
Release Date : 2019-03-16
The International Conference On Advanced Machine Learning Technologies And Applications Amlta2019 written by Aboul Ella Hassanien and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-03-16 with Computers categories.
This book presents the peer-reviewed proceedings of the 4th International Conference on Advanced Machine Learning Technologies and Applications (AMLTA 2019), held in Cairo, Egypt, on March 28–30, 2019, and organized by the Scientific Research Group in Egypt (SRGE). The papers cover the latest research on machine learning, deep learning, biomedical engineering, control and chaotic systems, text mining, summarization and language identification, machine learning in image processing, renewable energy, cyber security, and intelligence swarms and optimization.