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Statistical Genomics

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Cover of 'Statistical Genomics'

Table of Contents

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    Book Overview
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    Chapter 1 Overview of Sequence Data Formats
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    Chapter 2 Integrative Exploratory Analysis of Two or More Genomic Datasets
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    Chapter 3 Study Design for Sequencing Studies
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    Chapter 4 Genomic Annotation Resources in R/Bioconductor
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    Chapter 5 The Gene Expression Omnibus Database
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    Chapter 6 A Practical Guide to The Cancer Genome Atlas (TCGA)
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    Chapter 7 Working with Oligonucleotide Arrays
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    Chapter 8 Meta-Analysis in Gene Expression Studies
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    Chapter 9 Practical Analysis of Genome Contact Interaction Experiments
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    Chapter 10 Quantitative Comparison of Large-Scale DNA Enrichment Sequencing Data
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    Chapter 11 Variant Calling From Next Generation Sequence Data
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    Chapter 12 Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes
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    Chapter 13 NGS-QC Generator: A Quality Control System for ChIP-Seq and Related Deep Sequencing-Generated Datasets
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    Chapter 14 Operating on Genomic Ranges Using BEDOPS
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    Chapter 15 GMAP and GSNAP for Genomic Sequence Alignment: Enhancements to Speed, Accuracy, and Functionality
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    Chapter 16 Visualizing Genomic Data Using Gviz and Bioconductor
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    Chapter 17 Introducing Machine Learning Concepts with WEKA
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    Chapter 18 Experimental Design and Power Calculation for RNA-seq Experiments
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    Chapter 19 It’s DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR
Attention for Chapter 4: Genomic Annotation Resources in R/Bioconductor
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Chapter title
Genomic Annotation Resources in R/Bioconductor
Chapter number 4
Book title
Statistical Genomics
Published in
Methods in molecular biology, January 2016
DOI 10.1007/978-1-4939-3578-9_4
Pubmed ID
Book ISBNs
978-1-4939-3576-5, 978-1-4939-3578-9
Authors

Marc R. J. Carlson, Hervé Pagès, Sonali Arora, Valerie Obenchain, Martin Morgan, Carlson, Marc R. J., Pagès, Hervé, Arora, Sonali, Obenchain, Valerie, Morgan, Martin

Editors

Ewy Mathé, Sean Davis

Abstract

Annotation resources make up a significant proportion of the Bioconductor project (Huber et al., Nat Methods 12:115-121, 2015). And there are also a diverse set of online resources available which are accessed using specific packages. Here we describe the most popular of these resources and give some high level examples on how to use them.

Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 11 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Sweden 1 9%
Germany 1 9%
Unknown 9 82%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 4 36%
Researcher 2 18%
Professor 1 9%
Student > Doctoral Student 1 9%
Student > Bachelor 1 9%
Other 1 9%
Unknown 1 9%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 3 27%
Agricultural and Biological Sciences 2 18%
Mathematics 1 9%
Medicine and Dentistry 1 9%
Neuroscience 1 9%
Other 1 9%
Unknown 2 18%