Search results for: r-bioinformatics-cookbook

R Bioinformatics Cookbook

Author : Dan MacLean
File Size : 78.30 MB
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Over 60 recipes to model and handle real-life biological data using modern libraries from the R ecosystem Key Features Apply modern R packages to handle biological data using real-world examples Represent biological data with advanced visualizations suitable for research and publications Handle real-world problems in bioinformatics such as next-generation sequencing, metagenomics, and automating analyses Book Description Handling biological data effectively requires an in-depth knowledge of machine learning techniques and computational skills, along with an understanding of how to use tools such as edgeR and DESeq. With the R Bioinformatics Cookbook, you’ll explore all this and more, tackling common and not-so-common challenges in the bioinformatics domain using real-world examples. This book will use a recipe-based approach to show you how to perform practical research and analysis in computational biology with R. You will learn how to effectively analyze your data with the latest tools in Bioconductor, ggplot, and tidyverse. The book will guide you through the essential tools in Bioconductor to help you understand and carry out protocols in RNAseq, phylogenetics, genomics, and sequence analysis. As you progress, you will get up to speed with how machine learning techniques can be used in the bioinformatics domain. You will gradually develop key computational skills such as creating reusable workflows in R Markdown and packages for code reuse. By the end of this book, you’ll have gained a solid understanding of the most important and widely used techniques in bioinformatic analysis and the tools you need to work with real biological data. What you will learn Employ Bioconductor to determine differential expressions in RNAseq data Run SAMtools and develop pipelines to find single nucleotide polymorphisms (SNPs) and Indels Use ggplot to create and annotate a range of visualizations Query external databases with Ensembl to find functional genomics information Execute large-scale multiple sequence alignment with DECIPHER to perform comparative genomics Use d3.js and Plotly to create dynamic and interactive web graphics Use k-nearest neighbors, support vector machines and random forests to find groups and classify data Who this book is for This book is for bioinformaticians, data analysts, researchers, and R developers who want to address intermediate-to-advanced biological and bioinformatics problems by learning through a recipe-based approach. Working knowledge of R programming language and basic knowledge of bioinformatics are prerequisites.

Bioinformatics with R Cookbook

Author : Paurush Praveen
File Size : 50.68 MB
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This book is an easy-to-follow, stepwise guide to handle real life Bioinformatics problems. Each recipe comes with a detailed explanation to the solution steps. A systematic approach, coupled with lots of illustrations, tips, and tricks will help you as a reader grasp even the trickiest of concepts without difficulty.This book is ideal for computational biologists and bioinformaticians with basic knowledge of R programming, bioinformatics and statistics. If you want to understand various critical concepts needed to develop your computational models in Bioinformatics, then this book is for you. Basic knowledge of R is expected.

Bioinformatics with R Cookbook

Author : Paurush Praveen Sinha
File Size : 45.44 MB
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This book is an easy-to-follow, stepwise guide to handle real life Bioinformatics problems. Each recipe comes with a detailed explanation to the solution steps. A systematic approach, coupled with lots of illustrations, tips, and tricks will help you as a reader grasp even the trickiest of concepts without difficulty.This book is ideal for computational biologists and bioinformaticians with basic knowledge of R programming, bioinformatics and statistics. If you want to understand various critical concepts needed to develop your computational models in Bioinformatics, then this book is for you. Basic knowledge of R is expected.

Machine Learning with R Cookbook

Author : Yu-Wei, Chiu (David Chiu)
File Size : 69.81 MB
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The R language is a powerful open source functional programming language. At its core, R is a statistical programming language that provides impressive tools to analyze data and create high-level graphics. This book covers the basics of R by setting up a user-friendly programming environment and performing data ETL in R. Data exploration examples are provided that demonstrate how powerful data visualization and machine learning is in discovering hidden relationships. You will then dive into important machine learning topics, including data classification, regression, clustering, association rule mining, and dimension reduction.

Bioinformatics with Python Cookbook

Author : Tiago Antao
File Size : 49.68 MB
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If you are either a computational biologist or a Python programmer, you will probably relate to the expression "explosive growth, exciting times". Python is arguably the main programming language for big data, and the deluge of data in biology, mostly from genomics and proteomics, makes bioinformatics one of the most exciting fields in data science. Using the hands-on recipes in this book, you'll be able to do practical research and analysis in computational biology with Python. We cover modern, next-generation sequencing libraries and explore real-world examples on how to handle real data. The main focus of the book is the practical application of bioinformatics, but we also cover modern programming techniques and frameworks to deal with the ever increasing deluge of bioinformatics data.

R for Data Science Cookbook

Author : Yu-Wei, Chiu (David Chiu)
File Size : 53.33 MB
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Over 100 hands-on recipes to effectively solve real-world data problems using the most popular R packages and techniques About This Book Gain insight into how data scientists collect, process, analyze, and visualize data using some of the most popular R packages Understand how to apply useful data analysis techniques in R for real-world applications An easy-to-follow guide to make the life of data scientist easier with the problems faced while performing data analysis Who This Book Is For This book is for those who are already familiar with the basic operation of R, but want to learn how to efficiently and effectively analyze real-world data problems using practical R packages. What You Will Learn Get to know the functional characteristics of R language Extract, transform, and load data from heterogeneous sources Understand how easily R can confront probability and statistics problems Get simple R instructions to quickly organize and manipulate large datasets Create professional data visualizations and interactive reports Predict user purchase behavior by adopting a classification approach Implement data mining techniques to discover items that are frequently purchased together Group similar text documents by using various clustering methods In Detail This cookbook offers a range of data analysis samples in simple and straightforward R code, providing step-by-step resources and time-saving methods to help you solve data problems efficiently. The first section deals with how to create R functions to avoid the unnecessary duplication of code. You will learn how to prepare, process, and perform sophisticated ETL for heterogeneous data sources with R packages. An example of data manipulation is provided, illustrating how to use the “dplyr” and “data.table” packages to efficiently process larger data structures. We also focus on “ggplot2” and show you how to create advanced figures for data exploration. In addition, you will learn how to build an interactive report using the “ggvis” package. Later chapters offer insight into time series analysis on financial data, while there is detailed information on the hot topic of machine learning, including data classification, regression, clustering, association rule mining, and dimension reduction. By the end of this book, you will understand how to resolve issues and will be able to comfortably offer solutions to problems encountered while performing data analysis. Style and approach This easy-to-follow guide is full of hands-on examples of data analysis with R. Each topic is fully explained beginning with the core concept, followed by step-by-step practical examples, and concluding with detailed explanations of each concept used.

R Cookbook

Author : Paul Teetor
File Size : 37.61 MB
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With more than 200 practical recipes, this book helps you perform data analysis with R quickly and efficiently. The R language provides everything you need to do statistical work, but its structure can be difficult to master. This collection of concise, task-oriented recipes makes you productive with R immediately, with solutions ranging from basic tasks to input and output, general statistics, graphics, and linear regression. Each recipe addresses a specific problem, with a discussion that explains the solution and offers insight into how it works. If you’re a beginner, R Cookbook will help get you started. If you’re an experienced data programmer, it will jog your memory and expand your horizons. You’ll get the job done faster and learn more about R in the process. Create vectors, handle variables, and perform other basic functions Input and output data Tackle data structures such as matrices, lists, factors, and data frames Work with probability, probability distributions, and random variables Calculate statistics and confidence intervals, and perform statistical tests Create a variety of graphic displays Build statistical models with linear regressions and analysis of variance (ANOVA) Explore advanced statistical techniques, such as finding clusters in your data "Wonderfully readable, R Cookbook serves not only as a solutions manual of sorts, but as a truly enjoyable way to explore the R language—one practical example at a time."—Jeffrey Ryan, software consultant and R package author

Machine Learning with R Cookbook

Author : AshishSingh Bhatia
File Size : 43.98 MB
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Explore over 110 recipes to analyze data and build predictive models with simple and easy-to-use R code About This Book Apply R to simplify predictive modeling with short and simple code Use machine learning to solve problems ranging from small to big data Build a training and testing dataset, applying different classification methods. Who This Book Is For This book is for data science professionals, data analysts, or people who have used R for data analysis and machine learning who now wish to become the go-to person for machine learning with R. Those who wish to improve the efficiency of their machine learning models and need to work with different kinds of data set will find this book very insightful. What You Will Learn Create and inspect transaction datasets and perform association analysis with the Apriori algorithm Visualize patterns and associations using a range of graphs and find frequent item-sets using the Eclat algorithm Compare differences between each regression method to discover how they solve problems Detect and impute missing values in air quality data Predict possible churn users with the classification approach Plot the autocorrelation function with time series analysis Use the Cox proportional hazards model for survival analysis Implement the clustering method to segment customer data Compress images with the dimension reduction method Incorporate R and Hadoop to solve machine learning problems on big data In Detail Big data has become a popular buzzword across many industries. An increasing number of people have been exposed to the term and are looking at how to leverage big data in their own businesses, to improve sales and profitability. However, collecting, aggregating, and visualizing data is just one part of the equation. Being able to extract useful information from data is another task, and a much more challenging one. Machine Learning with R Cookbook, Second Edition uses a practical approach to teach you how to perform machine learning with R. Each chapter is divided into several simple recipes. Through the step-by-step instructions provided in each recipe, you will be able to construct a predictive model by using a variety of machine learning packages. In this book, you will first learn to set up the R environment and use simple R commands to explore data. The next topic covers how to perform statistical analysis with machine learning analysis and assess created models, covered in detail later on in the book. You'll also learn how to integrate R and Hadoop to create a big data analysis platform. The detailed illustrations provide all the information required to start applying machine learning to individual projects. With Machine Learning with R Cookbook, machine learning has never been easier. Style and approach This is an easy-to-follow guide packed with hands-on examples of machine learning tasks. Each topic includes step-by-step instructions on tackling difficulties faced when applying R to machine learning.

R Graphics Cookbook

Author : Winston Chang
File Size : 78.77 MB
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"Practical recipes for visualizing data"--Cover.

R Cookbook

Author : JD Long
File Size : 27.38 MB
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Perform data analysis with R quickly and efficiently with more than 275 practical recipes in this expanded second edition. The R language provides everything you need to do statistical work, but its structure can be difficult to master. These task-oriented recipes make you productive with R immediately. Solutions range from basic tasks to input and output, general statistics, graphics, and linear regression. Each recipe addresses a specific problem and includes a discussion that explains the solution and provides insight into how it works. If you’re a beginner, R Cookbook will help get you started. If you’re an intermediate user, this book will jog your memory and expand your horizons. You’ll get the job done faster and learn more about R in the process. Create vectors, handle variables, and perform basic functions Simplify data input and output Tackle data structures such as matrices, lists, factors, and data frames Work with probability, probability distributions, and random variables Calculate statistics and confidence intervals and perform statistical tests Create a variety of graphic displays Build statistical models with linear regressions and analysis of variance (ANOVA) Explore advanced statistical techniques, such as finding clusters in your data

R Recipes for Analysis Visualization and Machine Learning

Author : Viswa Viswanathan
File Size : 65.50 MB
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Get savvy with R language and actualize projects aimed at analysis, visualization and machine learning About This Book Proficiently analyze data and apply machine learning techniques Generate visualizations, develop interactive visualizations and applications to understand various data exploratory functions in R Construct a predictive model by using a variety of machine learning packages Who This Book Is For This Learning Path is ideal for those who have been exposed to R, but have not used it extensively yet. It covers the basics of using R and is written for new and intermediate R users interested in learning. This Learning Path also provides in-depth insights into professional techniques for analysis, visualization, and machine learning with R – it will help you increase your R expertise, regardless of your level of experience. What You Will Learn Get data into your R environment and prepare it for analysis Perform exploratory data analyses and generate meaningful visualizations of the data Generate various plots in R using the basic R plotting techniques Create presentations and learn the basics of creating apps in R for your audience Create and inspect the transaction dataset, performing association analysis with the Apriori algorithm Visualize associations in various graph formats and find frequent itemset using the ECLAT algorithm Build, tune, and evaluate predictive models with different machine learning packages Incorporate R and Hadoop to solve machine learning problems on big data In Detail The R language is a powerful, open source, functional programming language. At its core, R is a statistical programming language that provides impressive tools to analyze data and create high-level graphics. This Learning Path is chock-full of recipes. Literally! It aims to excite you with awesome projects focused on analysis, visualization, and machine learning. We'll start off with data analysis – this will show you ways to use R to generate professional analysis reports. We'll then move on to visualizing our data – this provides you with all the guidance needed to get comfortable with data visualization with R. Finally, we'll move into the world of machine learning – this introduces you to data classification, regression, clustering, association rule mining, and dimension reduction. This Learning Path combines some of the best that Packt has to offer in one complete, curated package. It includes content from the following Packt products: R Data Analysis Cookbook by Viswa Viswanathan and Shanthi Viswanathan R Data Visualization Cookbook by Atmajitsinh Gohil Machine Learning with R Cookbook by Yu-Wei, Chiu (David Chiu) Style and approach This course creates a smooth learning path that will teach you how to analyze data and create stunning visualizations. The step-by-step instructions provided for each recipe in this comprehensive Learning Path will show you how to create machine learning projects with R.

Practical Data Science Cookbook

Author : Prabhanjan Tattar
File Size : 82.7 MB
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Over 85 recipes to help you complete real-world data science projects in R and Python About This Book Tackle every step in the data science pipeline and use it to acquire, clean, analyze, and visualize your data Get beyond the theory and implement real-world projects in data science using R and Python Easy-to-follow recipes will help you understand and implement the numerical computing concepts Who This Book Is For If you are an aspiring data scientist who wants to learn data science and numerical programming concepts through hands-on, real-world project examples, this is the book for you. Whether you are brand new to data science or you are a seasoned expert, you will benefit from learning about the structure of real-world data science projects and the programming examples in R and Python. What You Will Learn Learn and understand the installation procedure and environment required for R and Python on various platforms Prepare data for analysis by implement various data science concepts such as acquisition, cleaning and munging through R and Python Build a predictive model and an exploratory model Analyze the results of your model and create reports on the acquired data Build various tree-based methods and Build random forest In Detail As increasing amounts of data are generated each year, the need to analyze and create value out of it is more important than ever. Companies that know what to do with their data and how to do it well will have a competitive advantage over companies that don't. Because of this, there will be an increasing demand for people that possess both the analytical and technical abilities to extract valuable insights from data and create valuable solutions that put those insights to use. Starting with the basics, this book covers how to set up your numerical programming environment, introduces you to the data science pipeline, and guides you through several data projects in a step-by-step format. By sequentially working through the steps in each chapter, you will quickly familiarize yourself with the process and learn how to apply it to a variety of situations with examples using the two most popular programming languages for data analysis—R and Python. Style and approach This step-by-step guide to data science is full of hands-on examples of real-world data science tasks. Each recipe focuses on a particular task involved in the data science pipeline, ranging from readying the dataset to analytics and visualization

Python Machine Learning Cookbook

Author : Giuseppe Ciaburro
File Size : 48.85 MB
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Discover powerful ways to effectively solve real-world machine learning problems using key libraries including scikit-learn, TensorFlow, and PyTorch Key Features Learn and implement machine learning algorithms in a variety of real-life scenarios Cover a range of tasks catering to supervised, unsupervised and reinforcement learning techniques Find easy-to-follow code solutions for tackling common and not-so-common challenges Book Description This eagerly anticipated second edition of the popular Python Machine Learning Cookbook will enable you to adopt a fresh approach to dealing with real-world machine learning and deep learning tasks. With the help of over 100 recipes, you will learn to build powerful machine learning applications using modern libraries from the Python ecosystem. The book will also guide you on how to implement various machine learning algorithms for classification, clustering, and recommendation engines, using a recipe-based approach. With emphasis on practical solutions, dedicated sections in the book will help you to apply supervised and unsupervised learning techniques to real-world problems. Toward the concluding chapters, you will get to grips with recipes that teach you advanced techniques including reinforcement learning, deep neural networks, and automated machine learning. By the end of this book, you will be equipped with the skills you need to apply machine learning techniques and leverage the full capabilities of the Python ecosystem through real-world examples. What you will learn Use predictive modeling and apply it to real-world problems Explore data visualization techniques to interact with your data Learn how to build a recommendation engine Understand how to interact with text data and build models to analyze it Work with speech data and recognize spoken words using Hidden Markov Models Get well versed with reinforcement learning, automated ML, and transfer learning Work with image data and build systems for image recognition and biometric face recognition Use deep neural networks to build an optical character recognition system Who this book is for This book is for data scientists, machine learning developers, deep learning enthusiasts and Python programmers who want to solve real-world challenges using machine-learning techniques and algorithms. If you are facing challenges at work and want ready-to-use code solutions to cover key tasks in machine learning and the deep learning domain, then this book is what you need. Familiarity with Python programming and machine learning concepts will be useful.

Exploiting Maine Faire Experimental Data for Gene finding in Plasmodium Falciparum Using Random Forests

Author : Christopher Wilks
File Size : 61.52 MB
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Bioinformatics for Geneticists

Author : Michael R. Barnes
File Size : 70.68 MB
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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.

Linux Powerful Server Administration

Author : Uday R. Sawant
File Size : 58.79 MB
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Get hands-on recipes to make the most of Ubuntu Server, CentOS 7 Linux Server and RHEL 7 Server About This Book Get Linux servers up and running in seconds, In-depth guide to explore new features and solutions in server administration Maintain performance and security of your server solution by deploying expert configuration advice Who This Book Is For This Learning Path is intended for system administrators with a basic understanding of Linux operating systems and written with the novice-to-intermediate Linux user in mind. To get the most of this Learning Path, you should have a working knowledge of basic system administration and management tools. What You Will Learn Set up high performance, scalable, and fault-tolerant back ends with web and database servers Facilitate team communication with a real-time chat service and collaboration tools Monitor, manage and develop your server's file system to maintain a stable performance Gain best practice methods on sharing files and resources through a network Install and configure common standard services such as web, mail, FTP, database and domain name server technologies Create kickstart scripts to automatically deploy RHEL 7 systems Use Orchestration and configuration management tools to manage your environment In Detail Linux servers are frequently selected over other server operating systems for their stability, security and flexibility advantages.This Learning Path will teach you how to get up and running with three of the most popular Linux server distros: Ubuntu Server, CentOS 7 Server, and RHEL 7 Server. We will begin with the Ubuntu Server and show you how to make the most of Ubuntu's advanced functionalities. Moving on, we will provide you with all the knowledge that will give you access to the inner workings of the latest CentOS version 7. Finally, touching RHEL 7, we will provide you with solutions to common RHEL 7 Server challenges.This Learning Path combines some of the best that Packt has to offer in one complete, curated package. It includes content from the following Packt products: 1) Ubuntu Server Cookbook 2) CentOS 7 Linux Server Cookbook, Second Edition 3) Red Hat Enterprise Linux Server Cookbook Style and approach This easy-to-follow practical guide contains hands on examples and solutions to real word administration problems and problems faced when building your RHEL 7 system from scratch using orchestration tools.

Biotechnology

Author : Hans-Jürgen Rehm
File Size : 37.74 MB
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Book Review Index

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Technometrics

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Books in Print 2009 2010

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