Bioinformatics with R Cookbook

Author: Paurush Praveen Sinha

Publisher: Packt Publishing Ltd

ISBN: 1783283149

Category: Computers

Page: 340

View: 7184

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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.
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Bioinformatics with R Cookbook

Author: Paurush Praveen

Publisher: Packt Pub Limited

ISBN: 9781783283132

Category: Computers

Page: 340

View: 1649

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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.
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Machine Learning with R Cookbook

Author: Yu-Wei, Chiu (David Chiu)

Publisher: Packt Publishing Ltd

ISBN: 1783982055

Category: Computers

Page: 442

View: 1781

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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.
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R Bioinformatics Cookbook

Use R and Bioconductor to perform RNAseq, genomics, data visualization, and bioinformatic analysis

Author: Dan MacLean

Publisher: Packt Publishing Ltd

ISBN: 1789955599

Category: Computers

Page: 316

View: 867

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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.
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Bioinformatics with Python Cookbook

Author: Tiago Antao

Publisher: Packt Publishing Ltd

ISBN: 1783558652

Category: Computers

Page: 306

View: 1307

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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.
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Machine Learning with R Cookbook

Analyze data and build predictive models

Author: AshishSingh Bhatia,Yu-Wei, Chiu (David Chiu)

Publisher: Packt Publishing Ltd

ISBN: 1787287807

Category: Computers

Page: 572

View: 4124

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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.
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R Data Visualization Cookbook

Author: Atmajitsinh Gohil

Publisher: Packt Publishing Ltd

ISBN: 1783989513

Category: Computers

Page: 236

View: 8015

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If you are a data journalist, academician, student or freelance designer who wants to learn about data visualization, this book is for you. Basic knowledge of R programming is expected.
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R for Data Science Cookbook

Author: Yu-Wei, Chiu (David Chiu)

Publisher: Packt Publishing Ltd

ISBN: 1784392049

Category: Computers

Page: 452

View: 668

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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.
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R Cookbook

Proven Recipes for Data Analysis, Statistics, and Graphics

Author: Paul Teetor

Publisher: "O'Reilly Media, Inc."

ISBN: 9781449307264

Category: Computers

Page: 438

View: 5415

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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
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R: Recipes for Analysis, Visualization and Machine Learning

Author: Viswa Viswanathan,Shanthi Viswanathan,Atmajitsinh Gohil,Yu-Wei, Chiu (David Chiu)

Publisher: Packt Publishing Ltd

ISBN: 178728879X

Category: Computers

Page: 959

View: 4512

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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.
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