building bioinformatics solutions with perl r and mysql

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Building Bioinformatics Solutions 2nd Edition

Author : Conrad Bessant
ISBN : 9780199658558
Genre : Computers
File Size : 59. 94 MB
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This book introduces the reader to all the key concepts and technologies needed to begin developing their own bioinformatics tools. The new edition includes more bioinformatics-specific content and a new chapter on good software engineering practices to help people working in teams.

Developing Bioinformatics Computer Skills

Author : Cynthia Gibas
ISBN : 1565926641
Genre : Computers
File Size : 72. 81 MB
Format : PDF, Kindle
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Offers a structured approach to biological data and the computer tools needed to analyze it, covering UNIX, databases, computation, Perl, data mining, data visualization, and tailoring software to suit specific research needs.

Introduction To Data Mining For The Life Sciences

Author : Rob Sullivan
ISBN : 9781597452908
Genre : Science
File Size : 30. 97 MB
Format : PDF
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Data mining provides a set of new techniques to integrate, synthesize, and analyze tdata, uncovering the hidden patterns that exist within. Traditionally, techniques such as kernel learning methods, pattern recognition, and data mining, have been the domain of researchers in areas such as artificial intelligence, but leveraging these tools, techniques, and concepts against your data asset to identify problems early, understand interactions that exist and highlight previously unrealized relationships through the combination of these different disciplines can provide significant value for the investigator and her organization.

Primer To Analysis Of Genomic Data Using R

Author : Cedric Gondro
ISBN : 9783319144757
Genre : Medical
File Size : 23. 90 MB
Format : PDF
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Through this book, researchers and students will learn to use R for analysis of large-scale genomic data and how to create routines to automate analytical steps. The philosophy behind the book is to start with real world raw datasets and perform all the analytical steps needed to reach final results. Though theory plays an important role, this is a practical book for graduate and undergraduate courses in bioinformatics and genomic analysis or for use in lab sessions. How to handle and manage high-throughput genomic data, create automated workflows and speed up analyses in R is also taught. A wide range of R packages useful for working with genomic data are illustrated with practical examples. The key topics covered are association studies, genomic prediction, estimation of population genetic parameters and diversity, gene expression analysis, functional annotation of results using publically available databases and how to work efficiently in R with large genomic datasets. Important principles are demonstrated and illustrated through engaging examples which invite the reader to work with the provided datasets. Some methods that are discussed in this volume include: signatures of selection, population parameters (LD, FST, FIS, etc); use of a genomic relationship matrix for population diversity studies; use of SNP data for parentage testing; snpBLUP and gBLUP for genomic prediction. Step-by-step, all the R code required for a genome-wide association study is shown: starting from raw SNP data, how to build databases to handle and manage the data, quality control and filtering measures, association testing and evaluation of results, through to identification and functional annotation of candidate genes. Similarly, gene expression analyses are shown using microarray and RNAseq data. At a time when genomic data is decidedly big, the skills from this book are critical. In recent years R has become the de facto tool for analysis of gene expression data, in addition to its prominent role in analysis of genomic data. Benefits to using R include the integrated development environment for analysis, flexibility and control of the analytic workflow. Included topics are core components of advanced undergraduate and graduate classes in bioinformatics, genomics and statistical genetics. This book is also designed to be used by students in computer science and statistics who want to learn the practical aspects of genomic analysis without delving into algorithmic details. The datasets used throughout the book may be downloaded from the publisher’s website./p

A Handbook Of Statistical Analyses Using R Third Edition

Author : Torsten Hothorn
ISBN : 9781482204599
Genre : Mathematics
File Size : 22. 70 MB
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Like the best-selling first two editions, A Handbook of Statistical Analyses using R, Third Edition provides an up-to-date guide to data analysis using the R system for statistical computing. The book explains how to conduct a range of statistical analyses, from simple inference to recursive partitioning to cluster analysis. New to the Third Edition Three new chapters on quantile regression, missing values, and Bayesian inference Extra material in the logistic regression chapter that describes a regression model for ordered categorical response variables Additional exercises More detailed explanations of R code New section in each chapter summarizing the results of the analyses Updated version of the HSAUR package (HSAUR3), which includes some slides that can be used in introductory statistics courses Whether you’re a data analyst, scientist, or student, this handbook shows you how to easily use R to effectively evaluate your data. With numerous real-world examples, it emphasizes the practical application and interpretation of results.

Rna Seq Data Analysis

Author : Eija Korpelainen
ISBN : 9781466595019
Genre : Mathematics
File Size : 85. 6 MB
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The State of the Art in Transcriptome Analysis RNA sequencing (RNA-seq) data offers unprecedented information about the transcriptome, but harnessing this information with bioinformatics tools is typically a bottleneck. RNA-seq Data Analysis: A Practical Approach enables researchers to examine differential expression at gene, exon, and transcript levels and to discover novel genes, transcripts, and whole transcriptomes. Balanced Coverage of Theory and Practice Each chapter starts with theoretical background, followed by descriptions of relevant analysis tools and practical examples. Accessible to both bioinformaticians and nonprogramming wet lab scientists, the examples illustrate the use of command-line tools, R, and other open source tools, such as the graphical Chipster software. The Tools and Methods to Get Started in Your Lab Taking readers through the whole data analysis workflow, this self-contained guide provides a detailed overview of the main RNA-seq data analysis methods and explains how to use them in practice. It is suitable for researchers from a wide variety of backgrounds, including biology, medicine, genetics, and computer science. The book can also be used in a graduate or advanced undergraduate course.

Bioinformatics Computing

Author : Bryan P. Bergeron
ISBN : 0131008250
Genre : Computers
File Size : 51. 24 MB
Format : PDF
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Comprehensive and concise, this handbook has chapters on computing visualization, large database designs, advanced pattern matching and other key bioinformatics techniques. It is a practical guide to computing in the growing field of Bioinformatics--the study of how information is represented and transmitted in biological systems, starting at the molecular level.

Visualization Of Time Oriented Data

Author : Wolfgang Aigner
ISBN : 0857290797
Genre : Computers
File Size : 29. 65 MB
Format : PDF, Kindle
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Time is an exceptional dimension that is common to many application domains such as medicine, engineering, business, or science. Due to the distinct characteristics of time, appropriate visual and analytical methods are required to explore and analyze them. This book starts with an introduction to visualization and historical examples of visual representations. At its core, the book presents and discusses a systematic view of the visualization of time-oriented data along three key questions: what is being visualized (data), why something is visualized (user tasks), and how it is presented (visual representation). To support visual exploration, interaction techniques and analytical methods are required that are discussed in separate chapters. A large part of this book is devoted to a structured survey of 101 different visualization techniques as a reference for scientists conducting related research as well as for practitioners seeking information on how their time-oriented data can best be visualized.

Pentaho Kettle Solutions

Author : Matt Casters
ISBN : 0470947527
Genre : Computers
File Size : 44. 21 MB
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A complete guide to Pentaho Kettle, the Pentaho Data lntegration toolset for ETL This practical book is a complete guide to installing, configuring, and managing Pentaho Kettle. If you’re a database administrator or developer, you’ll first get up to speed on Kettle basics and how to apply Kettle to create ETL solutions—before progressing to specialized concepts such as clustering, extensibility, and data vault models. Learn how to design and build every phase of an ETL solution. Shows developers and database administrators how to use the open-source Pentaho Kettle for enterprise-level ETL processes (Extracting, Transforming, and Loading data) Assumes no prior knowledge of Kettle or ETL, and brings beginners thoroughly up to speed at their own pace Explains how to get Kettle solutions up and running, then follows the 34 ETL subsystems model, as created by the Kimball Group, to explore the entire ETL lifecycle, including all aspects of data warehousing with Kettle Goes beyond routine tasks to explore how to extend Kettle and scale Kettle solutions using a distributed “cloud” Get the most out of Pentaho Kettle and your data warehousing with this detailed guide—from simple single table data migration to complex multisystem clustered data integration tasks.

Bioinformatics With R Cookbook

Author : Paurush Praveen Sinha
ISBN : 9781783283149
Genre : Computers
File Size : 55. 28 MB
Format : PDF, Mobi
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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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