Computational Genomics with R

Computational Genomics with R
Author: Altuna Akalin
Publisher: CRC Press
Total Pages: 463
Release: 2020-12-16
Genre: Mathematics
ISBN: 1498781861
GET BOOK

Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.

Interactive Data Visualization with Python

Interactive Data Visualization with Python
Author: Abha Belorkar
Publisher: Packt Publishing Ltd
Total Pages: 362
Release: 2020-04-14
Genre: Computers
ISBN: 1800201060
GET BOOK

Create your own clear and impactful interactive data visualizations with the powerful data visualization libraries of Python Key FeaturesStudy and use Python interactive libraries, such as Bokeh and PlotlyExplore different visualization principles and understand when to use which oneCreate interactive data visualizations with real-world dataBook Description With so much data being continuously generated, developers, who can present data as impactful and interesting visualizations, are always in demand. Interactive Data Visualization with Python sharpens your data exploration skills, tells you everything there is to know about interactive data visualization in Python. You'll begin by learning how to draw various plots with Matplotlib and Seaborn, the non-interactive data visualization libraries. You'll study different types of visualizations, compare them, and find out how to select a particular type of visualization to suit your requirements. After you get a hang of the various non-interactive visualization libraries, you'll learn the principles of intuitive and persuasive data visualization, and use Bokeh and Plotly to transform your visuals into strong stories. You'll also gain insight into how interactive data and model visualization can optimize the performance of a regression model. By the end of the course, you'll have a new skill set that'll make you the go-to person for transforming data visualizations into engaging and interesting stories. What you will learnExplore and apply different interactive data visualization techniquesManipulate plotting parameters and styles to create appealing plotsCustomize data visualization for different audiencesDesign data visualizations using interactive librariesUse Matplotlib, Seaborn, Altair and Bokeh for drawing appealing plotsCustomize data visualization for different scenariosWho this book is for This book intends to provide a solid training ground for Python developers, data analysts and data scientists to enable them to present critical data insights in a way that best captures the user's attention and imagination. It serves as a simple step-by-step guide that demonstrates the different types and components of visualization, the principles, and techniques of effective interactivity, as well as common pitfalls to avoid when creating interactive data visualizations. Students should have an intermediate level of competency in writing Python code, as well as some familiarity with using libraries such as pandas.

Data Analysis for the Life Sciences with R

Data Analysis for the Life Sciences with R
Author: Rafael A. Irizarry
Publisher: CRC Press
Total Pages: 537
Release: 2016-10-04
Genre: Mathematics
ISBN: 1498775861
GET BOOK

This book covers several of the statistical concepts and data analytic skills needed to succeed in data-driven life science research. The authors proceed from relatively basic concepts related to computed p-values to advanced topics related to analyzing highthroughput data. They include the R code that performs this analysis and connect the lines of code to the statistical and mathematical concepts explained.

Genomics Data Analysis for Crop Improvement

Genomics Data Analysis for Crop Improvement
Author: Priyanka Anjoy
Publisher: Springer Nature
Total Pages: 378
Release: 2024-02-10
Genre: Technology & Engineering
ISBN: 9819969131
GET BOOK

This book addresses complex problems associated with crop improvement programs, using a wide range of programming solutions, for genomics data handling and sustainable agriculture. It describes important concepts in genomics data analysis and sequence-based mapping approaches along with references. The book contains 16 chapters on recent developments in several methods of genomic data analysis for crop improvements and sustainable agriculture, all authored by eminent researchers who are experts in their fields. These chapters focus on applications of a wide range of key bioinformatics topics, including assembly, annotation, and visualization of next-generation sequencing (NGS) data; expression profiles of coding and noncoding RNA; statistical and quantitative genetics; trait-based association analysis, quantitative trait loci (QTL) mapping, and artificial intelligence in genomic studies. Real examples and case studies in the book will come in handy when applying the techniques. The relative scarcity of reference materials covering bioinformatics applications as compared with the readily available books also enhances the utility of this book. The targeted readers of the book are scientists, researchers, and bioinformaticians from genomics and advanced breeding in different areas. The book will appeal to the applied researchers engaged in crop improvements and sustainable agriculture by using bioinformatics tools, students, research project leaders, and practitioners from the various marginal disciplines and interdisciplinary research.

Data Analysis and Visualization in Genomics and Proteomics

Data Analysis and Visualization in Genomics and Proteomics
Author: Francisco Azuaje
Publisher: John Wiley & Sons
Total Pages: 284
Release: 2005-06-24
Genre: Science
ISBN: 0470094400
GET BOOK

Data Analysis and Visualization in Genomics and Proteomics is the first book addressing integrative data analysis and visualization in this field. It addresses important techniques for the interpretation of data originating from multiple sources, encoded in different formats or protocols, and processed by multiple systems. One of the first systematic overviews of the problem of biological data integration using computational approaches This book provides scientists and students with the basis for the development and application of integrative computational methods to analyse biological data on a systemic scale Places emphasis on the processing of multiple data and knowledge resources, and the combination of different models and systems

The Kiwifruit Genome

The Kiwifruit Genome
Author: Raffaele Testolin
Publisher: Springer
Total Pages: 275
Release: 2016-05-02
Genre: Science
ISBN: 3319322745
GET BOOK

This book describes the basic botanical features of kiwifruit and its wild relatives, reports on the steps that led to its genome sequencing, and discusses the results obtained with the assembly and annotation. The core chapters provide essential insights into the main gene families that characterize this species as a crop, including the genes controlling sugar and starch metabolism, pigment biosynthesis and degradation, the ascorbic-acid pathway, fruit softening and postharvest metabolism, allergens, and resistance to pests and diseases. The book offers a valuable reference guide for taxonomists, geneticists and horticulturists. Further, since information gained from the genome sequence is extraordinarily useful in assessing the breeding value of individuals based on whole-genome scans, it will especially benefit plant breeders. Accordingly, chapters are included that focus on gene introgression from wild relatives and genome-based breeding.

Interactive Web-Based Data Visualization with R, plotly, and shiny

Interactive Web-Based Data Visualization with R, plotly, and shiny
Author: Carson Sievert
Publisher: CRC Press
Total Pages: 278
Release: 2020-01-30
Genre: Business & Economics
ISBN: 0429824203
GET BOOK

The richly illustrated Interactive Web-Based Data Visualization with R, plotly, and shiny focuses on the process of programming interactive web graphics for multidimensional data analysis. It is written for the data analyst who wants to leverage the capabilities of interactive web graphics without having to learn web programming. Through many R code examples, you will learn how to tap the extensive functionality of these tools to enhance the presentation and exploration of data. By mastering these concepts and tools, you will impress your colleagues with your ability to quickly generate more informative, engaging, and reproducible interactive graphics using free and open source software that you can share over email, export to pdf, and more. Key Features: Convert static ggplot2 graphics to an interactive web-based form Link, animate, and arrange multiple plots in standalone HTML from R Embed, modify, and respond to plotly graphics in a shiny app Learn best practices for visualizing continuous, discrete, and multivariate data Learn numerous ways to visualize geo-spatial data This book makes heavy use of plotly for graphical rendering, but you will also learn about other R packages that support different phases of a data science workflow, such as tidyr, dplyr, and tidyverse. Along the way, you will gain insight into best practices for visualization of high-dimensional data, statistical graphics, and graphical perception. The printed book is complemented by an interactive website where readers can view movies demonstrating the examples and interact with graphics.