Bioinformatics With R Cookbook
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R Bioinformatics Cookbook
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Author : Dan MacLean
language : en
Publisher:
Release Date : 2019-10-11
R Bioinformatics Cookbook written by Dan MacLean and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-10-11 with Computers categories.
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
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Author : Paurush Praveen
language : en
Publisher:
Release Date : 2014
Bioinformatics With R Cookbook written by Paurush Praveen and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014 with Bioinformatics categories.
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.
Bioinformatics With R Cookbook
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Author : Paurush Praveen Sinha
language : en
Publisher:
Release Date : 2014-01-01
Bioinformatics With R Cookbook written by Paurush Praveen Sinha and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-01-01 with categories.
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.
R Bioinformatics Cookbook
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Author : Dan MacLean
language : en
Publisher: Packt Publishing Ltd
Release Date : 2023-10-31
R Bioinformatics Cookbook written by Dan MacLean and has been published by Packt Publishing Ltd this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-10-31 with Computers categories.
Discover over 80 recipes for modeling and handling real-life biological data using modern libraries from the R ecosystem Key Features Apply modern R packages to process biological data using real-world examples Represent biological data with advanced visualizations and workflows suitable for research and publications Solve real-world bioinformatics problems such as transcriptomics, genomics, and phylogenetics Purchase of the print or Kindle book includes a free PDF eBook Book DescriptionThe updated second edition of R Bioinformatics Cookbook takes a recipe-based approach to show you how to conduct practical research and analysis in computational biology with R. You’ll learn how to create a useful and modular R working environment, along with loading, cleaning, and analyzing data using the most up-to-date Bioconductor, ggplot2, and tidyverse tools. This book will walk you through the Bioconductor tools necessary for you to understand and carry out protocols in RNA-seq and ChIP-seq, phylogenetics, genomics, gene search, gene annotation, statistical analysis, and sequence analysis. As you advance, you'll find out how to use Quarto to create data-rich reports, presentations, and websites, as well as get a clear understanding of how machine learning techniques can be applied in the bioinformatics domain. The concluding chapters will help you develop proficiency in key skills, such as gene annotation analysis and functional programming in purrr and base R. Finally, you'll discover how to use the latest AI tools, including ChatGPT, to generate, edit, and understand R code and draft workflows for complex analyses. By the end of this book, you'll have gained a solid understanding of the skills and techniques needed to become a bioinformatics specialist and efficiently work with large and complex bioinformatics datasets.What you will learn Set up a working environment for bioinformatics analysis with R Import, clean, and organize bioinformatics data using tidyr Create publication-quality plots, reports, and presentations using ggplot2 and Quarto Analyze RNA-seq, ChIP-seq, genomics, and next-generation genetics with Bioconductor Search for genes and proteins by performing phylogenetics and gene annotation Apply ML techniques to bioinformatics data using mlr3 Streamline programmatic work using iterators and functional tools in the base R and purrr packages Use ChatGPT to create, annotate, and debug code and workflows 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 via a recipe-based approach. Working knowledge of the R programming language and basic knowledge of bioinformatics are prerequisites.
R Bioinformatics Cookbook
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Author : Dan MacLean
language : en
Publisher: Packt Publishing Ltd
Release Date : 2019-10-11
R Bioinformatics Cookbook written by Dan MacLean and has been published by Packt Publishing Ltd this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-10-11 with Science categories.
Over 60 recipes to model and handle real-life biological data using modern libraries from the R ecosystem Key FeaturesApply modern R packages to handle biological data using real-world examplesRepresent biological data with advanced visualizations suitable for research and publicationsHandle real-world problems in bioinformatics such as next-generation sequencing, metagenomics, and automating analysesBook 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 learnEmploy Bioconductor to determine differential expressions in RNAseq dataRun SAMtools and develop pipelines to find single nucleotide polymorphisms (SNPs) and IndelsUse ggplot to create and annotate a range of visualizationsQuery external databases with Ensembl to find functional genomics informationExecute large-scale multiple sequence alignment with DECIPHER to perform comparative genomicsUse d3.js and Plotly to create dynamic and interactive web graphicsUse k-nearest neighbors, support vector machines and random forests to find groups and classify dataWho 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
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Author : Paurush Praveen Sinha
language : en
Publisher:
Release Date : 2014
Bioinformatics With R Cookbook written by Paurush Praveen Sinha and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014 with categories.
Machine Learning With R Cookbook
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Author : Chiu Yu-Wei
language : en
Publisher:
Release Date : 2015
Machine Learning With R Cookbook written by Chiu Yu-Wei and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015 with Mathematical statistics categories.
If you want to learn how to use R for machine learning and gain insights from your data, then this book is ideal for you. Regardless of your level of experience, this book covers the basics of applying R to machine learning through to advanced techniques. While it is helpful if you are familiar with basic programming or machine learning concepts, you do not require prior experience to benefit from this book.
R For Data Science Cookbook
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Author : Yu-Wei, Chiu (David Chiu)
language : en
Publisher: Packt Publishing Ltd
Release Date : 2016-07-29
R For Data Science Cookbook written by Yu-Wei, Chiu (David Chiu) and has been published by Packt Publishing Ltd this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-07-29 with Computers categories.
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
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Author : JD Long
language : en
Publisher: "O'Reilly Media, Inc."
Release Date : 2019-06-21
R Cookbook written by JD Long and has been published by "O'Reilly Media, Inc." this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-06-21 with Computers categories.
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
Machine Learning With R Cookbook
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Author : AshishSingh Bhatia
language : en
Publisher: Packt Publishing Ltd
Release Date : 2017-10-23
Machine Learning With R Cookbook written by AshishSingh Bhatia and has been published by Packt Publishing Ltd this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-10-23 with Computers categories.
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.