Title | Statistical Genomics [electronic resource] : Methods and Protocols / edited by Ewy Mathé, Sean Davis |
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Imprint | New York, NY : Springer New York : Imprint: Humana Press, 2016 |
Edition | 1st ed. 2016 |
Connect to | http://dx.doi.org/10.1007/978-1-4939-3578-9 |
Descript | XI, 418 p. 113 illus., 85 illus. in color. online resource |
Overview of Sequence Data Formats -- Integrative Exploratory Analysis of Two or More Genomic Datasets -- Study Design for Sequencing Studies -- Genomic Annotation Resources in R/Bioconductor -- The Gene Expression Omnibus Database -- A Practical Guide to the Cancer Genome Atlas (TCGA) -- Working with Oligonucleotide Arrays -- Meta-Analysis in Gene Expression Studies -- Practical Analysis of Genome Contact Interaction Experiments -- Quantitative Comparison of Large-Scale DNA Enrichment Sequencing Data -- Variant Calling From Next Generation Sequence Data -- Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes -- NGS-QC Generator: A Quality Control System for ChIP-seq and Related Deep Sequencing-Generated Datasets -- Operating on Genomic Ranges Using BEDOPS -- GMAP and GSNAP for Genomic Sequence Alignment: Enhancements to Speed, Accuracy, and Functionality -- Visualizing Genomic Data using Gviz and Bioconductor -- Introducing Machine Learning Concepts with WEKA -- Experimental Design and Power Calculation for RNA-Seq Experiments -- It’s DE-licious: A Recipe for Differential Expression Analyses of RNA-Seq Experiments Using Quasi-Likelihood Methods in EdgeR