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R Bioinformatics Cookbook
R Bioinformatics Cookbook

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

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Profile Icon MacLean Profile Icon Dr Dan Maclean
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$42.99 $47.99
Full star icon Full star icon Half star icon Empty star icon Empty star icon 2.7 (3 Ratings)
eBook Oct 2019 316 pages 1st Edition
eBook
$42.99 $47.99
Paperback
$59.99
Subscription
Free Trial
Renews at $19.99p/m
Arrow left icon
Profile Icon MacLean Profile Icon Dr Dan Maclean
Arrow right icon
$42.99 $47.99
Full star icon Full star icon Half star icon Empty star icon Empty star icon 2.7 (3 Ratings)
eBook Oct 2019 316 pages 1st Edition
eBook
$42.99 $47.99
Paperback
$59.99
Subscription
Free Trial
Renews at $19.99p/m
eBook
$42.99 $47.99
Paperback
$59.99
Subscription
Free Trial
Renews at $19.99p/m

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R Bioinformatics Cookbook

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Key benefits

  • 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

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.

Who is this book 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.

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

Product Details

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Publication date, Length, Edition, Language, ISBN-13
Publication date : Oct 11, 2019
Length: 316 pages
Edition : 1st
Language : English
ISBN-13 : 9781789955590
Vendor :
RStudio
Languages :
Concepts :
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What do you get with eBook?

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Product feature icon Download this book in EPUB and PDF formats
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Product Details

Publication date : Oct 11, 2019
Length: 316 pages
Edition : 1st
Language : English
ISBN-13 : 9781789955590
Vendor :
RStudio
Languages :
Concepts :
Tools :

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Table of Contents

12 Chapters
Performing Quantitative RNAseq Chevron down icon Chevron up icon
Finding Genetic Variants with HTS Data Chevron down icon Chevron up icon
Searching Genes and Proteins for Domains and Motifs Chevron down icon Chevron up icon
Phylogenetic Analysis and Visualization Chevron down icon Chevron up icon
Metagenomics Chevron down icon Chevron up icon
Proteomics from Spectrum to Annotation Chevron down icon Chevron up icon
Producing Publication and Web-Ready Visualizations Chevron down icon Chevron up icon
Working with Databases and Remote Data Sources Chevron down icon Chevron up icon
Useful Statistical and Machine Learning Methods Chevron down icon Chevron up icon
Programming with Tidyverse and Bioconductor Chevron down icon Chevron up icon
Building Objects and Packages for Code Reuse Chevron down icon Chevron up icon
Other Books You May Enjoy Chevron down icon Chevron up icon

Customer reviews

Rating distribution
Full star icon Full star icon Half star icon Empty star icon Empty star icon 2.7
(3 Ratings)
5 star 33.3%
4 star 0%
3 star 0%
2 star 33.3%
1 star 33.3%
sreechakilam Nov 16, 2020
Full star icon Full star icon Full star icon Full star icon Full star icon 5
like, very useful
Amazon Verified review Amazon
Cliente Amazon Jul 26, 2023
Full star icon Full star icon Empty star icon Empty star icon Empty star icon 2
Even for begginers it is pretty poor. Any tutorial in the internet may be more useful for the topics included in the book. It may be useful to get a general idea, but not to be introduced in practical bioinformatics
Amazon Verified review Amazon
RUser Jan 04, 2021
Full star icon Empty star icon Empty star icon Empty star icon Empty star icon 1
Hallo, dieses Buch leidet unter der Verwendung von R-Libraries, die zumindes zu Anfang des Jahres 2021 nicht funktionieren. Das ist immer der Tod von Cook Books! Hier handelt es sich um die für viele "Rezepte" essentielle Library gmapR, die beispielsweise für das Betriebssystem Windows nicht verfügbar ist (Stand Anfang 2021). Unter den neuesten Versionen von Ubuntu und R hat es aber auch nicht funktioniert.Schade, aber das ist natürlich immer eine Gefahr bei kostenloser Software, die - wie in diesem Falle R mit Bioconductor - irgendwann zu komplex wird, um zuverlässig zu funktionieren.Da nutzt dann auch das schönste Kochbuch nichts, wenn man kein Feuer im Herd hat.Ein Update: Ich gab dem Buch eine zweite Chance. Vergebens, der Code der (Stand Januar 2021) verfügbar war, enthält viele kleine Fehler (fehlerhafte Verweise auf Dateiverzeichnisse), die nur lästig sind, und schwere inhaltliche Fehler. Man kann den Code eventuell selbst korrigieren, dann braucht man aber das Buch nicht mehr... Das Recipe3.R des dritten Kapitels ist eine Zumutung. Wieder wird eine Library verwendet, die noch in der Entwicklung ist, und deren Herunterladen aufgrund vieler Abhängigkeiten reine Glückssache ist. Ich habe es nach mehreren Stunden aufgegeben. Und der Code, der das Herunterladen vereinfachen soll - ja: Code, um das komplexe Herunterladen überhaupt organisieren zu können - den kann man abschreiben. Er ist nicht in den zum Buch verfügbaren Codes enthalten. Viel Spaß dabei.Das Buch hätte eine Lücke füllen können, so füllt es eine Lücke im Altpapier. Der Verlag bedauert...
Amazon Verified review Amazon
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