Titlebook: Statistical Genomics; Methods and Protocol Ewy Mathé,Sean Davis Book 2016 Springer Science+Business Media New York 2016 sequence data forma

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Methods in Molecular Biologyhttp://image.papertrans.cn/s/image/876423.jpg

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https://doi.org/10.1007/978-1-4939-3578-9sequence data formats; omnibus database; oligonucleotide arrays; gene expression studies; genome contact

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Genomic Annotation Resources in R/BioconductorAnnotation 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.

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Overview of Sequence Data FormatsVarious file formats have been introduced/developed in order to store and manipulate this information. This chapter presents an overview of the file formats including FASTQ, FASTA, SAM/BAM, GFF/GTF, BED, and VCF that are commonly used in analysis of next-generation sequencing data.

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A Practical Guide to The Cancer Genome Atlas (TCGA) and made available genomic sequence, expression, methylation, and copy number variation data on over 11,000 individuals who represent over 30 different types of cancer. This chapter provides a brief overview of the TCGA program and detailed instructions and tips for investigators on how to find, access, and download this data.

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The Gene Expression Omnibus Databases various Web-based tools and strategies that enable users to locate data relevant to their specific interests, as well as to visualize and analyze the data. This chapter includes detailed descriptions of methods to query and download GEO data and use the analysis and visualization tools. The GEO homepage is at ..

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Study Design for Sequencing Studiesty and low bias. High-throughput sequencing has therefore become the primary data acquisition method for many genomics studies and is being used more and more to address molecular biology questions. By applying principles of statistical experimental design, sequencing experiments can be made more se