Bioinformatics Data Skills by Oreilly——学习生信的入门好书

最新推荐文章于 2024-11-06 10:10:41 发布
最新推荐文章于 2024-11-06 10:10:41 发布
阅读量3.3k 收藏 20
点赞数 8
分类专栏： bioinformatics 文章标签： bioinformatics data skills by oreil
版权声明：本文为博主原创文章，遵循 CC 4.0 BY-SA 版权协议，转载请附上原文出处链接和本声明。
本文链接：https://blog.csdn.net/weixin_42953727/article/details/99999415
版权

翻阅《生信宝典》公众号，偶然看到推荐的两本生信入门好书，分享给大家：

  1. 《Bioinformatics Data Skills - - Reproducible.and.Robust.Research.with.Open.Source.Tools》链接:》链接: 接: https://pan.baidu.com/s/1c2g0MPU 密码: 密码: v2c9
  2. 《Bioinformatics with Python Cookbook》链接: 接: https://pan.baidu.com/s/1dF0H52x 密码: 密码: a7e4

自己看了其中比较初级版本的《Bioinformatics Data Skills》的第一章（简介部分），全书500多页，虽然是全英文，但是通俗易懂，适合对Linux、Python（文本处理语言）等有一些基本了解的新手学习。

若对两者不太了解，本书又推荐了一些有用的书籍，如：
用于Python学习的：Bioinformatics Programming
Using Python by Mitchell L. Model (O’Reilly, 2009), Learning Python, 5th Edition,by Mark Lutz (O’Reilly, 2013), and Python in a Nutshell, 2nd, by Alex Martelli(O’Reilly, 2006)
用于了解Unix命令的： Practical Computing for Biologists
by Steven Haddock and Casey Dunn (Sinauer, 2010) or UNIX and Perl to the Rescue by Keith Bradnam and Ian Korf (Cambridge University Press, 2012).
关于正则表达式的运用：Introducing Regular Expressions by Michael Fitzgerald (O’Reilly) ；http://regex101.com and http://www.debug‐gex.com to write,test and debug regular expressions.

Supplementary Material on GitHub
本书的附加材料在GitHub上可以获得（Chapter 5 中介绍）。

Computing Resources and Setup
若是Mac环境，作者推荐使用Homebrew帮助你进行软件的安装。有条件的最好是在Linux或Unix环境下，进行测试

Organization of This Book
共分为三大部分：
Part I, containing one chapter on ideology;
Part II, which covers the basics of getting started with a bioinformatics project;
Part III, which covers bioinformatics data skills.
Chapter2. trivial topic, organized project, markdown
Chapter3. Unix
Chapter4. increase productivity when working with remote machines.
Chapter5. Git
Chapter6. download data, validate integrity
Part III 第七章之后是实战
Chapter7. Unix data tools, Unix pipelines
Chapter8. R language
Chapter9. genomic data
Chapter10. sequence data FASTA, FASTQ
Chapter11. SAM,BAM,Samtools,variant calling
Chapter12. data-processing scripts and pipelines(Bash scriptin, find and xargs)
Chapter13. Tabix, SQL, GWAS
Chapter14. further develop

We have a web page for this book, where we list errata, examples, and any additional information. You can access this page at http://bit.ly/Bio-DS.

读书笔记---Bioinformatics Data Skills
cfc424的博客
12-23 1097
读书笔记---Bioinformatics Data Skills
Bioinformatics Data Skills by Oreilly学习笔记-6
weixin_42953727的博客
08-25 520
Chapter6 Bioinformatics Data Retrieving Bioinformatics Data Downloading Data with wget and curl Two common command-line programs for downloading data from the Web are wget and curl. Depending on your ...
Bioinformatics Data Skills by Oreilly学习笔记-1
weixin_42953727的博客
08-22 535
Chapter1. How to learn bioinformatics 看起来是琐碎的小技巧，甚至是关于信仰的东西，可能要真正投入进去，才能慢慢体会，看得不太认真，许多略过的东西，以后可以再回头看。 Test Code, or Better Yet, Let Code Test Code 学到了用Code test code: ...
Bioinformatics.Data.Skills.Reproducible.and.Robust.Research.pdf
08-21
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
Bioinformatics Data Skills by Oreilly学习笔记-10
weixin_42953727的博客
09-03 642
Chapter 10 Working with Sequence Data Nucleotide (and protein) sequences are stored in two plain-text formats widespread in bioinformatics: FASTA and FASTQ—pronounced fast-ah (or fast-A) and fast-Q, r...
Bioinformatics Data Skills by Oreilly学习笔记-7-3
weixin_42953727的博客
08-31 276
接上一篇Chapter7 Text Processing with Awk Two basic concepts——records and fields, and pattern-action pairs Assigns the entire record to the variable $0, and field one’s value is assigned to $1, field two’...
Bioinformatics Data Skills by Oreilly学习笔记-11-1
weixin_42953727的博客
09-08 789
Chapter 11 Working with Alignment Data 突然觉得这是一本比较基础的且要有耐心才能看下去的书，但作者介绍的比较繁琐，没有直入主题，基本的分析流程和背景并不太成体系。有基础的人甚至可以直接跳到11章，想快点看完进入下一本了。 The Sequence Alignment/ Mapping (SAM) format for mapping data (and its...
Bioinformatics Data Skills by Oreilly学习笔记-3
weixin_42953727的博客
08-24 400
Chapter 3 Remedial Unix Shell == In this chapter, we’ll cover remedial concepts that deeply underly how we use the shell in bioinformatics: streams, redirection, pipes, working with running programs,...
Bioinformatics Data Skills by Oreilly学习笔记-12
weixin_42953727的博客
09-13 435
Chapter12 Bioinformatics Shell Scripting, Writing Pipelines, and Parallelizing Tasks We’ll see how to write rerunnable Bash shell scripts, automate fileprocessing tasks with find and xargs, run pipeli...
Bioinformatics Data Skills by Oreilly学习笔记-7-1
weixin_42953727的博客
08-26 414
PART III Practice: Bioinformatics Data Skills Chapter7 Unix Data Tools Inspecting and Manipulating Text Data with Unix Tools In this chapter, we’ll work with very simple genomic feature formats: BED (...
Bioinformatics Data Skills Reproducible and Robust Research with Open 无水印pdf
09-28
Bioinformatics Data Skills Reproducible and Robust Research with Open Source Tools 英文无水印pdf pdf所有页面使用FoxitReader和PDF-XChangeViewer测试都可以打开 本资源转载自网络，如有侵权，请联系上传者或csdn删除 本资源转载自网络，如有侵权，请联系上传者或csdn删除
Bioinformatics Data Skills Reproducible and Robust Research with Open azw3
09-28
Bioinformatics Data Skills Reproducible and Robust Research with Open Source Tools 英文azw3 本资源转载自网络，如有侵权，请联系上传者或csdn删除 本资源转载自网络，如有侵权，请联系上传者或csdn删除
Bioinformatics Data Skills Reproducible and Robust Research with Open mobi
09-28
Bioinformatics Data Skills Reproducible and Robust Research with Open Source Tools 英文mobi 本资源转载自网络，如有侵权，请联系上传者或csdn删除 本资源转载自网络，如有侵权，请联系上传者或csdn删除
bioinformatics skills
10-08
bioinformatics skills bioinformatics skills bioinformatics skills bioinformatics skills
Bioinformatics Data Skills Reproducible and Robust Research with Open epub
09-28
Bioinformatics Data Skills Reproducible and Robust Research with Open Source Tools 英文epub 本资源转载自网络，如有侵权，请联系上传者或csdn删除 本资源转载自网络，如有侵权，请联系上传者或csdn删除
Bioinformatics Data Skills by Oreilly学习笔记-9
weixin_42953727的博客
09-01 243
Chapter9 Working with Range Data A Crash Course in Genomic Ranges and Coordinate Systems CrossMap is a command-line tool that converts many data formats (BED, GFF/ GTF, SAM/BAM, Wiggle, VCF) between c...
Bioinformatics Data Skills by Oreilly学习笔记-11-2
weixin_42953727的博客
09-09 742
接上一篇Chapter 11 Visualizing Alignments with samtools tview and the Integrated Genomics Viewer Samtools tview requires position-sorted and indexed BAM files as input.
Bioinformatics Data Skills 项目常见问题解决方案
最新发布
gitblog_00024的博客
11-06 559
Bioinformatics Data Skills 项目常见问题解决方案 bds-files Supplementary files for my book, "Bioinformatics Data Skills" 项目地址:...
Bioinformatics Data Skills by Oreilly学习笔记-7-2
weixin_42953727的博客
08-29 403
接上一篇Chapter 7 The All-Powerful Grep grep “pattern” files –color=auto grep 是贪婪匹配，用**-w**进行准确匹配（constraining our matches to be words），默认输出行。 $ cat example.txt bio bioinfo bioinformatics computational ...
CRF入门：结构化预测的机器学习方法
它在机器学习领域中发挥着关键作用，尤其是在自然语言处理(Natural Language Processing, NLP)，计算机视觉(Computer Vision)，以及生物信息学(Bioinformatics)等多个应用领域。CRF的核心理念是将分类模型的能力与...
评论
添加红包

请填写红包祝福语或标题

个

红包个数最小为10个

元

红包金额最低5元

当前余额3.43元 前往充值 >
需支付：10.00元
成就一亿技术人!
领取后你会自动成为博主和红包主的粉丝 规则
hope_wisdom
发出的红包
实付元
使用余额支付
点击重新获取
扫码支付
钱包余额 0

抵扣说明：

1.余额是钱包充值的虚拟货币，按照1:1的比例进行支付金额的抵扣。
2.余额无法直接购买下载，可以购买VIP、付费专栏及课程。

余额充值