Statistical Genomics

Methods and Protocols

Buch | Hardcover

418 Seiten

2016 | 1st ed. 2016
Humana Press Inc. (Verlag)
978-1-4939-3576-5 (ISBN)

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This volume expands on statistical analysis of genomic data by discussing cross-cutting groundwork material, public data repositories, common applications, and representative tools for operating on genomic data. Statistical Genomics: Methods and Protocols is divided into four sections. The first section discusses overview material and resources that can be applied across topics mentioned throughout the book. The second section covers prominent public repositories for genomic data. The third section presents several different biological applications of statistical genomics, and the fourth section highlights software tools that can be used to facilitate ad-hoc analysis and data integration. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible analysis protocols, and tips on troubleshooting and avoiding known pitfalls.

Through and practical, Statistical Genomics: Methods and Protocols, explores a range of both applications and tools and is ideal for anyone interested in the statistical analysis of genomic data.

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.

Erscheinungsdatum	08.10.2016
Reihe/Serie	Methods in Molecular Biology ; 1418
Zusatzinfo	85 Illustrations, color; 28 Illustrations, black and white; XI, 418 p. 113 illus., 85 illus. in color.
Verlagsort	Totowa, NJ
Sprache	englisch
Maße	178 x 254 mm
Themenwelt	Informatik ► Weitere Themen ► Bioinformatik
	Medizin / Pharmazie ► Medizinische Fachgebiete
	Studium ► 2. Studienabschnitt (Klinik) ► Humangenetik
	Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
Schlagworte	bioconductor • gene expression studies • genome contact interaction experiments • genome-scale analysis • oligonucleotide arrays • omnibus database • RNA-seq experiments • sequence data formats
ISBN-10	1-4939-3576-3 / 1493935763
ISBN-13	978-1-4939-3576-5 / 9781493935765
Zustand	Neuware