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Bioinformatics.Data.Skills.Reproducible.and.Robust.Research.pdf
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上传时间: 2015-08-21
详细说明： This practical book teaches the skills that scientists need for turning large sequencing datasets into reproducible and robust biological findings. Many biologists begin their bioinformatics training by learning scripting languages like Python and R alongside the Unix command line. But there's a huge gap between knowing a few programming languages and being prepared to analyze large amounts of biological data. Rather than teach bioinformatics as a set of workflows that are likely to change with this rapidly evolving field, this book demsonstrates the practice of bioinformatics through data skills. Rigorous assessment of data quality and of the effectiveness of tools is the foundation of reproducible and robust bioinformatics analysis. Through open source and freely available tools, you'll learn not only how to do bioinformatics, but how to approach problems as a bioinformatician. Go from handling small problems with messy scripts to tackling large problems with clever methods and tools Focus on high-throughput (or "next generation") sequencing data Learn data analysis with modern methods, versus covering older theoretical concepts Understand how to choose and implement the best tool for the job Delve into methods that lead to easier, more reproducible, and robust bioinformatics analysis Table of Contents Part I. Ideology: Data Skills for Robust and Reproducible Bioinformatics Chapter 1. How to Learn Bioinformatics Part II. Prerequisites: Essential Skills for Getting Started with a Bioinformatics Project Chapter 2. Setting Up and Managing a Bioinformatics Project Chapter 3. Remedial Unix Shell Chapter 4. Working with Remote Machines Chapter 5. Git for Scientists Chapter 6. Bioinformatics Data Part III. Practice: Bioinformatics Data Skills Chapter 7. Unix Data Tools Chapter 8. A Rapid Introduction to the R Language Chapter 9. Working with Range Data Chapter 10. Working with Sequence Data Chapter 11. Working with Alignment Data Chapter 12. Bioinformatics Shell Scripting, Writing Pipelines, and Parallelizing Tasks Chapter 13. Out-of-Memory Approaches: Tabix and SQLite Chapter 14. Conclusion ...展开收缩
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