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A Primer In Biological Data Analysis And Visualization Using R

Author: Gregg Hartvigsen
Publisher: Columbia University Press
ISBN: 0231537042
Size: 52.62 MB
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R is the most widely used open-source statistical and programming environment for the analysis and visualization of biological data. Drawing on Gregg Hartvigsen's extensive experience teaching biostatistics and modeling biological systems, this text is an engaging, practical, and lab-oriented introduction to R for students in the life sciences. Underscoring the importance of R and RStudio in organizing, computing, and visualizing biological statistics and data, Hartvigsen guides readers through the processes of entering data into R, working with data in R, and using R to visualize data using histograms, boxplots, barplots, scatterplots, and other common graph types. He covers testing data for normality, defining and identifying outliers, and working with non-normal data. Students are introduced to common one- and two-sample tests as well as one- and two-way analysis of variance (ANOVA), correlation, and linear and nonlinear regression analyses. This volume also includes a section on advanced procedures and a chapter introducing algorithms and the art of programming using R.

Discrete Data Analysis With R

Author: Michael Friendly
Publisher: CRC Press
ISBN: 1498725856
Size: 13.90 MB
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An Applied Treatment of Modern Graphical Methods for Analyzing Categorical Data Discrete Data Analysis with R: Visualization and Modeling Techniques for Categorical and Count Data presents an applied treatment of modern methods for the analysis of categorical data, both discrete response data and frequency data. It explains how to use graphical methods for exploring data, spotting unusual features, visualizing fitted models, and presenting results. The book is designed for advanced undergraduate and graduate students in the social and health sciences, epidemiology, economics, business, statistics, and biostatistics as well as researchers, methodologists, and consultants who can use the methods with their own data and analyses. Along with describing the necessary statistical theory, the authors illustrate the practical application of the techniques to a large number of substantive problems, including how to organize data, conduct an analysis, produce informative graphs, and evaluate what the graphs reveal about the data. The first part of the book contains introductory material on graphical methods for discrete data, basic R skills, and methods for fitting and visualizing one-way discrete distributions. The second part focuses on simple, traditional nonparametric tests and exploratory methods for visualizing patterns of association in two-way and larger frequency tables. The final part of the text discusses model-based methods for the analysis of discrete data. Web Resource The data sets and R software used, including the authors’ own vcd and vcdExtra packages, are available at http://cran.r-project.org.

Bayesian Data Analysis In Ecology Using Linear Models With R Bugs And Stan

Author: Franzi Korner-Nievergelt
Publisher: Academic Press
ISBN: 0128016787
Size: 43.67 MB
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Bayesian Data Analysis in Ecology Using Linear Models with R, BUGS, and STAN examines the Bayesian and frequentist methods of conducting data analyses. The book provides the theoretical background in an easy-to-understand approach, encouraging readers to examine the processes that generated their data. Including discussions of model selection, model checking, and multi-model inference, the book also uses effect plots that allow a natural interpretation of data. Bayesian Data Analysis in Ecology Using Linear Models with R, BUGS, and STAN introduces Bayesian software, using R for the simple modes, and flexible Bayesian software (BUGS and Stan) for the more complicated ones. Guiding the ready from easy toward more complex (real) data analyses ina step-by-step manner, the book presents problems and solutions—including all R codes—that are most often applicable to other data and questions, making it an invaluable resource for analyzing a variety of data types. Introduces Bayesian data analysis, allowing users to obtain uncertainty measurements easily for any derived parameter of interest Written in a step-by-step approach that allows for eased understanding by non-statisticians Includes a companion website containing R-code to help users conduct Bayesian data analyses on their own data All example data as well as additional functions are provided in the R-package blmeco

R In A Nutshell

Author: Joseph Adler
Publisher: O'Reilly Germany
ISBN: 3897216507
Size: 42.88 MB
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Wozu sollte man R lernen? Da gibt es viele Gründe: Weil man damit natürlich ganz andere Möglichkeiten hat als mit einer Tabellenkalkulation wie Excel, aber auch mehr Spielraum als mit gängiger Statistiksoftware wie SPSS und SAS. Anders als bei diesen Programmen hat man nämlich direkten Zugriff auf dieselbe, vollwertige Programmiersprache, mit der die fertigen Analyse- und Visualisierungsmethoden realisiert sind – so lassen sich nahtlos eigene Algorithmen integrieren und komplexe Arbeitsabläufe realisieren. Und nicht zuletzt, weil R offen gegenüber beliebigen Datenquellen ist, von der einfachen Textdatei über binäre Fremdformate bis hin zu den ganz großen relationalen Datenbanken. Zudem ist R Open Source und erobert momentan von der universitären Welt aus die professionelle Statistik. R kann viel. Und Sie können viel mit R machen – wenn Sie wissen, wie es geht. Willkommen in der R-Welt: Installieren Sie R und stöbern Sie in Ihrem gut bestückten Werkzeugkasten: Sie haben eine Konsole und eine grafische Benutzeroberfläche, unzählige vordefinierte Analyse- und Visualisierungsoperationen – und Pakete, Pakete, Pakete. Für quasi jeden statistischen Anwendungsbereich können Sie sich aus dem reichen Schatz der R-Community bedienen. Sprechen Sie R! Sie müssen Syntax und Grammatik von R nicht lernen – wie im Auslandsurlaub kommen Sie auch hier gut mit ein paar aufgeschnappten Brocken aus. Aber es lohnt sich: Wenn Sie wissen, was es mit R-Objekten auf sich hat, wie Sie eigene Funktionen schreiben und Ihre eigenen Pakete schnüren, sind Sie bei der Analyse Ihrer Daten noch flexibler und effektiver. Datenanalyse und Statistik in der Praxis: Anhand unzähliger Beispiele aus Medizin, Wirtschaft, Sport und Bioinformatik lernen Sie, wie Sie Daten aufbereiten, mithilfe der Grafikfunktionen des lattice-Pakets darstellen, statistische Tests durchführen und Modelle anpassen. Danach werden Ihnen Ihre Daten nichts mehr verheimlichen.

Molecular Pathology

Author: William B. Coleman
Publisher: Academic Press
ISBN: 9780123859129
Size: 35.79 MB
Format: PDF, Kindle
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Molecular Pathology: The Molecular Basis of Human Disease provides a current and comprehensive view of the molecular basis and mechanisms of human disease. Combining accepted principles with broader theoretical concepts and with contributions from a group of experts, the book looks into disease processes in the context of traditional pathology and their implications for translational molecular medicine. It also discusses concepts in molecular biology and genetics, recent scientific and technological advances in modern pathology, the concept of ""molecular pathogenesis"" of disease, and how disease evolves from normal cells and tissues due to perturbations in molecular pathways. The book describes the integration of molecular and cellular pathogenesis using a bioinformatics approach and a systems biology approach to disease pathogenesis. It also discusses current and future strategies in molecular diagnosis of human disease, and the impact of molecular diagnosis on treatment decisions and the practice of personalized medicine. This book is a valuable resource for students, biomedical researchers, practicing physician-scientists who undertake disease-related basic science and translational research, and pathology residents and other postdoctoral fellows. * Exam Master® web site will host "Self-assessment" questions that students can use to study for the molecular section of the board exam * Companion Web Site – will host a complete set of PowerPoint slides: to include images from the book and additional images for teaching; course materials; lecture materials * Teaches from the perspective of “integrative systems biology, which encompasses the intersection of all molecular aspects of biology, as applied to understanding human disease * Outlines the principles and practice of molecular pathology * Explains the practice of “molecular medicine and the translational aspects of molecular pathology

A Primer For Computational Biology

Author: Shawn T. O'Neil
Publisher:
ISBN: 9780870719264
Size: 48.79 MB
Format: PDF, ePub
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A Primer for Computational Biology aims to provide life scientists and students the skills necessary for research in a data-rich world. The text covers accessing and using remote servers via the command-line, writing programs and pipelines for data analysis, and provides useful vocabulary for interdisciplinary work. The book is broken into three parts: Introduction to Unix/Linux: The command-line is the "natural environment" of scientific computing, and this part covers a wide range of topics, including logging in, working with files and directories, installing programs and writing scripts, and the powerful "pipe" operator for file and data manipulation. Programming in Python: Python is both a premier language for learning and a common choice in scientific software development. This part covers the basic concepts in programming (data types, if-statements and loops, functions) via examples of DNA-sequence analysis. This part also covers more complex subjects in software development such as objects and classes, modules, and APIs. Programming in R: The R language specializes in statistical data analysis, and is also quite useful for visualizing large datasets. This third part covers the basics of R as a programming language (data types, if-statements, functions, loops and when to use them) as well as techniques for large-scale, multi-test analyses. Other topics include S3 classes and data visualization with ggplot2.

R F R Dummies

Author: Andrie de Vries
Publisher: John Wiley & Sons
ISBN: 3527812520
Size: 50.76 MB
Format: PDF
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Wollen Sie auch die umfangreichen Möglichkeiten von R nutzen, um Ihre Daten zu analysieren, sind sich aber nicht sicher, ob Sie mit der Programmiersprache wirklich zurechtkommen? Keine Sorge - dieses Buch zeigt Ihnen, wie es geht - selbst wenn Sie keine Vorkenntnisse in der Programmierung oder Statistik haben. Andrie de Vries und Joris Meys zeigen Ihnen Schritt für Schritt und anhand zahlreicher Beispiele, was Sie alles mit R machen können und vor allem wie Sie es machen können. Von den Grundlagen und den ersten Skripten bis hin zu komplexen statistischen Analysen und der Erstellung aussagekräftiger Grafiken. Auch fortgeschrittenere Nutzer finden in diesem Buch viele Tipps und Tricks, die Ihnen die Datenauswertung erleichtern.

Statistik Workshop F R Programmierer

Author: Allen B. Downey
Publisher: O'Reilly Germany
ISBN: 3868993436
Size: 62.64 MB
Format: PDF, Docs
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Wenn Sie programmieren können, beherrschen Sie bereits Techniken, um aus Daten Wissen zu extrahieren. Diese kompakte Einführung in die Statistik zeigt Ihnen, wie Sie rechnergestützt, anstatt auf mathematischem Weg Datenanalysen mit Python durchführen können. Praktischer Programmier-Workshop statt grauer Theorie: Das Buch führt Sie anhand eines durchgängigen Fallbeispiels durch eine vollständige Datenanalyse -- von der Datensammlung über die Berechnung statistischer Kennwerte und Identifikation von Mustern bis hin zum Testen statistischer Hypothesen. Gleichzeitig werden Sie mit statistischen Verteilungen, den Regeln der Wahrscheinlichkeitsrechnung, Visualisierungsmöglichkeiten und vielen anderen Arbeitstechniken und Konzepten vertraut gemacht. Statistik-Konzepte zum Ausprobieren: Entwickeln Sie über das Schreiben und Testen von Code ein Verständnis für die Grundlagen von Wahrscheinlichkeitsrechnung und Statistik: Überprüfen Sie das Verhalten statistischer Merkmale durch Zufallsexperimente, zum Beispiel indem Sie Stichproben aus unterschiedlichen Verteilungen ziehen. Nutzen Sie Simulationen, um Konzepte zu verstehen, die auf mathematischem Weg nur schwer zugänglich sind. Lernen Sie etwas über Themen, die in Einführungen üblicherweise nicht vermittelt werden, beispielsweise über die Bayessche Schätzung. Nutzen Sie Python zur Bereinigung und Aufbereitung von Rohdaten aus nahezu beliebigen Quellen. Beantworten Sie mit den Mitteln der Inferenzstatistik Fragestellungen zu realen Daten.

Bioinformatics For Geneticists

Author: Michael R. Barnes
Publisher: John Wiley & Sons
ISBN: 0470026197
Size: 45.58 MB
Format: PDF
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Bioinformatics for geneticists describes the key bioinformatics and genetic analysis processes that are needed to identify human genetic determinants. Including SNP functional analysis and statistical genetics.

Statistical And Evolutionary Analysis Of Biological Networks

Author: Michael P. H. Stumpf
Publisher: World Scientific
ISBN: 1848164335
Size: 46.62 MB
Format: PDF, Kindle
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Networks provide a very useful way to describe a wide range of different data types in biology, physics and elsewhere. Apart from providing a convenient tool to visualize highly dependent data, networks allow stringent mathematical and statistical analysis. In recent years, much progress has been achieved to interpret various types of biological network data such as transcriptomic, metabolomic and protein interaction data as well as epidemiological data. Of particular interest is to understand the organization, complexity and dynamics of biological networks and how these are influenced by network evolution and functionality. This book reviews and explores statistical, mathematical and evolutionary theory and tools in the understanding of biological networks. The book is divided into comprehensive and self-contained chapters, each of which focuses on an important biological network type, explains concepts and theory and illustrates how these can be used to obtain insight into biologically relevant processes and questions. There are chapters covering metabolic, transcriptomic, protein interaction and epidemiological networks as well as chapters that deal with theoretical and conceptual material. The authors, who contribute to the book, are active, highly regarded and well-known in the network community.