Bioconductor case studies

Cover of: Bioconductor case studies |

Published by Springer in New York, NY .

Written in English

Read online

Subjects:

  • Bioconductor (Computer file),
  • Bioinformatics,
  • R (Computer program language)

Edition Notes

Includes bibliographical references (p. [271]-275) and index.

Book details

StatementFlorian Hahne ... [et al.].
SeriesUse R!
ContributionsHahne, Florian.
Classifications
LC ClassificationsQH324.2 .B5417 2008
The Physical Object
Paginationx, 283 p. :
Number of Pages283
ID Numbers
Open LibraryOL23152707M
ISBN 100387772391
ISBN 109780387772394
LC Control Number2008926129

Download Bioconductor case studies

Bioconductor Case Studies. Authors: Florian Hahne, Wolfgang Huber, Robert Gentleman, Seth Falcon. Released 17 July Bioconductor Case Studies (Use R!) Paperback – Illustrated, Aug by Florian Hahne (Author), Wolfgang Huber (Author) › Visit Amazon's Wolfgang Huber Page. Find all the books, read about the author, and more.

See search results for this author. Are Cited by: The book is a dynamic document. All the code shown can be executed on a local computer, and readers are able to reproduce every computation, figure, and table.

The authors of this book have longtime experience in teaching introductory and advanced courses to the application of Bioconductor software. Bioconductor Case Studies. Authors: Hahne, F., Huber, W., Gentleman, R., Falcon, S.

Each chapter of this book describes an analysis of real data using hands-on example driven approaches. Short exercises help in the learning process and invite more advanced considerations of key topics.

The book is a dynamic document. Buy Bioconductor Case Studies (): NHBS - Florian Hahne, Wolfgang Huber, Robert Gentleman and Seth Falcon, Springer Nature. Bioconductor software has become a standard tool for the analysis and comprehension of data from high-throughput genomics experiments.

Its application spans a broad field of technologies used in contemporary molecular biology. In this volume, the authors present a collection of cases to apply Bioconductor tools in the analysis Bioconductor case studies book microarray gene expression data.5/5(2).

2 Bioconductor Case Studies ne, but there are some exceptions: Figure of boxplots by groups uses a colour shading for no particular reason and fails to mention that the group sizes range from 2 to ;Cited by: Case study on microarray classification (M.

Dettling) From CEL files to a list of interesting genes (R. Irizarry) (R) Contact us:   Bioconductor Case Studies (Use R!) Bioconductor software has become a standard tool for the analysis and comprehension of data from high-throughput genomics experiments.

Medical books Bioconductor Case Studies. Its application spans a broad field of technologies used in contemporary molecular biology. Bioconductor Case Studies - Ebook written by Florian Hahne, Wolfgang Huber, Robert Gentleman, Seth Falcon. Read this book using Google Play Books app on your PC, android, iOS devices.

Download for offline reading, highlight, bookmark or take notes while you read Bioconductor Case Studies. Bioconductor Case Studies Florian Hahne Wolfgang Huber Robert Gentleman Seth Falcon Code Figures Solutions Bioconductor case studies book Home Errata Chapter 1 The ALL Data Set Chapter 2 R and Bioconductor.

Buy a cheap copy of Bioconductor Case Studies (Use R!) by Florian Hahne, Wolfgang Huber, Robert Gentleman, Seth Falcon - A gently used book at a great low price. Free shipping in the US. Discount books. Let the stories liv. The book is a dynamic document.

All the code shown can be executed on a local computer, and readers are able to reproduce every computation, figure, and table. 豆瓣成员常用的标签(共16个) Bioconductor Case Studies (Use R)的书评. Find many great new & used options and get the best deals for Use R. Ser.: Bioconductor Case Studies by Wolfgang Huber, Florian Hahne, Robert Gentleman and Seth Falcon (, Trade Paperback) at the best online prices at eBay.

Free shipping for many products. Bioconductor Case Studies: enlarge image. Each chapter of this book describes an analysis of real data using hands-on example driven approaches.

Short exercises help in the learning process and invite more advanced considerations of key topics. The book is a dynamic document. All the code shown can be executed on a local computer, and.

Dear list members, I wonder if you could recommend some good generic textbooks on analysing microarrays using R and Bioconductor.

I'm tempted by "Statistics and Data Analysis for Microarrays Using R and Bioconductor" by Chapman & Hall, but it's pricey and I would like to hear some opinions/alternatives before I commit.

Bioconductor Case Studies (Use R!) They are just awful writers. I have used the other official "Bioconductor" books too and they are equally awful too. 0 out of 3 is not a good record. Rather than try to make money off gullible public by peddling incremental and useless books, please try to write a book which will truly educate someone.

## ## acinar alpha beta delta duct endothelial ## 21 ## epsilon mesenchymal pp ## 3 80 All methods are illustrated with publicly available data, and a major section of the book is devoted to exposition of fully worked case studies. This book is more than a static collection of descriptive text, figures, and code examples that were run by the authors to produce the text; it is a dynamic document.

2 Case examples In this chapter, we will show, with five case examples, how to retrieve data from five public repositories and some basic analysis that can be performed on the data. We introduce the functions and packages in R /Bioconductor that can be used to perform specific queries, retrieval, and analysis, all within a single R session.

Book summary After the great expansion of genome-wide association studies, their scientific methodology and, notably, their data analysis has matured in recent years, and they are a keystone in large epidemiological studies.

Newcomers to the field are confronted with a. Bioconductor Case Studies I have been asked to recommend introductory books and resources to R and Bioconductor. My problem Benchmarking bioinformatics tools. I want to profile / benchmark bioinformatics tools in general (CPU time, memory usage, disk usage.

Omic Association Studies with R and Bioconductor. DOI link for Omic Association Studies with R and Bioconductor. Omic Association Studies with R and Bioconductor book. By Juan R. González, Alejandro Cáceres. Edition 1st Edition.

First Published Case examples. With Juan R. González, Alejandro Cáceres. View abstract. chapter. Buy Bioconductor Case Studies by Florian Hahne for $ at Mighty Ape NZ. Bioconductor software has become a standard tool for the analysis and comprehension of data from high-throughput genomics experiments.

Its application. Abstract. In this chapter we cover basic uses of R and begin working with Bioconductor datasets and tools.

Topics covered include simple R programming, R graphics, and working with environments as hash tables. We introduce the ExpressionSet class as an example for a basic Bioconductor structure used for holding genomic data, in this case expression microarray data.

Association analyses of transcriptomic data for case/control studies are performed to describe the differences in transcriptomic patterns between the groups of subjects.

The cancer genome atlas can be fully accessed and analyzed with R/Bioconductor. This book guides through practical bioinformatics data analysis using the Bioconductor toolkit, which is based on the statistical language R.

R itself is an open-source recreation of the language S-Plus. The Bioconductor is a collection of R-packages for the analysis of genomic and molecular biological data generated in high-throughput experiments.

Bioconductor version: Release () This workflow package provides, through its vignette, a complete case study analysis of an RNA-Seq experiment using the Rsubread and edgeR packages. The workflow starts from read alignment and continues on to data exploration, to differential expression and, finally, to pathway analysis.

‎Preview and download books by Robert Gentleman, including Bioconductor Case Studies, Bioinformatics and Computational Biology Solutions Using R and Bioconductor and many more. Robert Gentleman is the author of Bioinformatics and Computational Biology Solutions Using R and Bioconductor ( avg rating, 7 ratings, 0 reviews, pub /5(18).

The Bioconductor project is a widely used open source and open development platform for software for computational biology. It is a leading platform for doing data science in Genomics.

This book covers the core functionality needed to deploy Bioconductor on modern datasets, and will lay the foundation for you to learn and explore parts of the p. Hahne et al, Bioconductor Case Studies; Springer [Several fairly advanced examples using R and Bioconductor, emphasizing genomic data] Braun and Murdoch, A First Course in Statistical Programming with R, CUP [A different emphasis from the other books here, good for those new to.

Coordinated analysis of multiple samples. To facilitate the analysis of experiments and studies with multiple samples, Bioconductor defines the SummarizedExperiment class. The computed summaries for the ranges are compiled into a rectangular array whose rows correspond to the ranges and whose columns correspond to the different samples (Fig.

2).For a typical experiment, there can be tens. A Little Book of R For Biomedical Statistics, Release How to install R on non-Windows computers (eg. Macintosh or Linux com-puters) The instructions above are for installing R.

Bioconductor. Bioconductor supports various useful packages such as: ape package aids in analysis of phylogenetics and evolution, adegenet is useful for multivariate analysis of genetic markers, picante is useful for ecological studies, affy supports analysis of Affymetrix gene chip data at prob level, DEGseq is an R package for identifying differentially expressed genes from RNA sequence.

Hahne et al, Bioconductor Case Studies; Springer [Several fairly advanced examples using R and Bioconductor, emphasizing genomic data] Braun and Murdoch, A First Course in Statistical Programming with R, CUP [A different emphasis from the other books here, good for those new to programming].

The book intends to be introductory in explaining and programming elementary statistical concepts, thereby bridging the gap between high school levels and the specialized statistical literature. After studying this book readers have a sufficient background for Bioconductor Case Studies (Hahne et al., ) and Bioinformatics and Computational.

This analysis is inspired by an example in the slightly dated but excellent book Bioconductor Case Studies. Step 1: Prepare the data. The data itself is conveniently available in an R package called “ALL”. library(ALL) data(ALL) Let’s look at what exactly we are dealing with here. Taken from here and formatted with some perl 1 "The R Project for Statistical.

the one byHahne, Huber, Gentleman, and Falcon() on using Bioconductor. The book reviewed here is another such case study, a large and very intersting one, concentrating on. Search the world's most comprehensive index of full-text books.

My library.Bioconductor is a great platform accessible to you, and it is a community developed open software resource. By the end of this course, you will be able to use essential Bioconductor packages and get a grasp of its infrastructure and some built-in datasets.

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