Bioinformatics Data Skills
Reproducible and Robust Research with Open Source Tools
Publisher: O'Reilly Media
Final Release Date: July 2015
Pages: 538

Learn the data skills necessary for turning large sequencing datasets into reproducible and robust biological findings. With this practical guide, you’ll learn how to use freely available open source tools to extract meaning from large complex biological data sets.

At no other point in human history has our ability to understand life’s complexities been so dependent on our skills to work with and analyze data. This intermediate-level book teaches the general computational and data skills you need to analyze biological data. If you have experience with a scripting language like Python, you’re ready to get started.

  • Go from handling small problems with messy scripts to tackling large problems with clever methods and tools
  • Process bioinformatics data with powerful Unix pipelines and data tools
  • Learn how to use exploratory data analysis techniques in the R language
  • Use efficient methods to work with genomic range data and range operations
  • Work with common genomics data file formats like FASTA, FASTQ, SAM, and BAM
  • Manage your bioinformatics project with the Git version control system
  • Tackle tedious data processing tasks with with Bash scripts and Makefiles
Table of Contents
Product Details
About the Author
Colophon
Recommended for You
Customer Reviews

REVIEW SNAPSHOT®

by PowerReviews
oreillyBioinformatics Data Skills
 
4.8

(based on 13 reviews)

Ratings Distribution

  • 5 Stars

     

    (11)

  • 4 Stars

     

    (1)

  • 3 Stars

     

    (1)

  • 2 Stars

     

    (0)

  • 1 Stars

     

    (0)

100%

of respondents would recommend this to a friend.

Pros

  • Helpful examples (11)
  • Easy to understand (10)
  • Well-written (9)
  • Concise (7)
  • Accurate (5)

Cons

No Cons

Best Uses

  • Intermediate (10)
  • Novice (10)
  • Student (6)
    • Reviewer Profile:
    • Student (3)

Reviewed by 13 customers

Sort by

Displaying reviews 1-10

Back to top

Previous | Next »

(3 of 3 customers found this review helpful)

 
5.0

All things you do need know to make reproducible research

By gunzapper

from Milano - Italy

Verified Reviewer

Pros

  • Accurate
  • Concise
  • Easy to understand
  • Helpful examples
  • Well-written

Cons

    Best Uses

    • Intermediate
    • Novice

    Comments about oreilly Bioinformatics Data Skills:

    This is the book that if you would do bioinformatics, or in general, reproducible research, have to read immediately. Because inside there are the explanations of all the tools that you have to use and you must to know.
    And there is no day that I don't consult this book, or the associated github repository, an exhaustive appendix of the book itself.

    (Note: the author probably is a big fan of Futurama, because on his github profile it is possible to read how have a futurama quotes every time you start a shell - this increase my respect for him).

    When I bought this book I thought "I looked other books with inside their title the word 'bioinformatics' - always I was unattended - always they was or too basic either focused on a pair of algorithms like the Blast one". But this time was different.

    I started to do bioinformatics - Hi, I am a biologist, nice to meet you IT people - by myself, in the hard way - without knowing exactly what this mean. I started form an hard programming language (C++)(Note: now I prefer Python), I learned to use CVS and the unit tests. I have appreciated to use Unix-like OS and the shells.
    But often I listen people give me bad advices: "Why you don't use windows, it is more simple. What about spreadsheets are more useful, why do you this instead of that - aka the simplest way?" and so on...

    After I read this book I understood that the way to do reproducible research is that I have started, I have been on the right side, but I did not understand why and I did not know all tools and hacks described in the book.

    (2 of 2 customers found this review helpful)

     
    5.0

    Clear and concise

    By sam

    from Lyon, FRANCE

    About Me Student

    Verified Reviewer

    Pros

    • Concise
    • Easy to understand
    • Helpful examples
    • Well-written

    Cons

      Best Uses

      • Intermediate
      • Novice

      Comments about oreilly Bioinformatics Data Skills:

      It gives you a basic overview of some of the most useful tools to study biological data. Without going into avoidable details, it goes straight to the point, and introduce you to the tools, so that you know they exist, how to use them, and how to know more about them.
      With an emphasize on reproducibility and good practices, the author does a great job at explaining common mistakes and how to avoid them.
      A must read for someone —not utterly— new to the field !

      (2 of 20 customers found this review helpful)

       
      3.0

      Many basic English errors

      By zerotimer

      from Wisconsin

      Comments about oreilly Bioinformatics Data Skills:

      I am reading the book at safari books online and noticing many grammatical as well as some missing English words. Some editor to clean this book up!

      Since I haven't finished it(no way close to it), I can't say anything about the usefulness yet. The choice of topics is excellent and I am looking forward to eventually buying it.

      (4 of 5 customers found this review helpful)

       
      4.0

      Fantastic DIY course textbook

      By Simon B

      from UK

      About Me Student

      Verified Buyer

      Pros

      • Easy to understand
      • Helpful examples
      • Well-written

      Cons

        Best Uses

        • Novice
        • Student

        Comments about oreilly Bioinformatics Data Skills:

        Superb book for those looking to develop bioinformatics skills. Covers loads of the supporting skills that are generally learnt through years of experience and aren't obvious in other textx/courses.

        Should be required reading for any PhD students or lab scientist working with data.

        (4 of 4 customers found this review helpful)

         
        5.0

        Best Bioinformatics Book

        By Mgollery

        from Lake Tahoe

        About Me Bioinformaticist

        Verified Buyer

        Pros

        • Concise
        • Easy to understand
        • Helpful examples

        Cons

          Best Uses

          • Expert
          • Intermediate
          • Novice
          • Student

          Comments about oreilly Bioinformatics Data Skills:

          This is the best bioinformatics book that I have seen. It gives you an introduction to the most necessary tools in the arsenal of the practicing Bioinformaticist. UNIX, R, Git, shell scripting, sequence files, alignment files.

          Of course, it doesn't have everything. But it gives you the essential skills to get things done. Not a lot of wasted space on theory or history.

          If you want to do Bioinformatics, you want to get this book.

          (4 of 4 customers found this review helpful)

           
          5.0

          Real-life bioinformatics

          By Gur

          from Israel

          Verified Reviewer

          Pros

          • Accurate
          • Concise
          • Easy to understand
          • Helpful examples
          • Well-written

          Cons

            Best Uses

            • Intermediate
            • Novice
            • Student

            Comments about oreilly Bioinformatics Data Skills:

            Reading halfway through (so far), I can best describe this book as a roadmap with stepping stones and practical tips to how *any biologist* can use computational power and bioinformatics for every day research tasks.
            From learning bioinformatics from scratch, I found most books I read to be focused on a specific topic or language, but lacking a bigger view of "real-life" bioinformatic projects with start, middle and end, including many other aspects that one should consider.
            This book is the first one I came across that does just that. It lays the framework of how to approach a project, covers important topics for managing a complete project, and refer to further resources if one needs to dig deeper into a specific aspect.
            I wish this book was available two years ago when I first started my graduate studies - It literally could have saved me a year.

            (3 of 3 customers found this review helpful)

             
            5.0

            Recommended to PhDs and post-docs alike

            By Peter

            from UK

            About Me Developer

            Verified Buyer

            Pros

            • Accurate
            • Concise
            • Easy to understand
            • Helpful examples
            • Well-written

            Cons

              Best Uses

              • Intermediate
              • Novice

              Comments about oreilly Bioinformatics Data Skills:

              I've not read all the book yet (the early release isn't even finished yet), but Vince has done a great job with this.

              I will be recommending it to future PhD students and early post-docs, as well as colleagues who like myself may have learnt much of this material the hard way, but are bound to find some little gems they've not seen before.

              I've mostly looked at the PDF edition, which with full page layout as expected in the printed version, looks very good. However, my initial inspection of some of the eBook formats show many of the code and data samples will struggle with narrow page layouts forcing line wrapping. That is incredible difficult to deal with through.

              (5 of 5 customers found this review helpful)

               
              5.0

              Full of great programmatic tricks

              By KATS

              from Minneapolis, MN

              About Me Developer, Educator

              Verified Buyer

              Pros

              • Accurate
              • Easy to understand
              • Helpful examples
              • Well-written

              Cons

                Best Uses

                • Expert
                • Intermediate

                Comments about oreilly Bioinformatics Data Skills:

                I have been programming in a UNIX environment for 26 years, and a leader in bioinformatics since I entered the field in 1998, and was surprised to find that I was able to learn useful tips and tricks in nearly every Chapter. We selected this book as the basis of a discussion group at our University and it is perfect. Very glad this book exists so I didn't have to write it myself!

                (3 of 3 customers found this review helpful)

                 
                5.0

                a very good read

                By crazyhottommy

                from Gainesville, FL

                About Me Phd Student, Student

                Verified Reviewer

                Pros

                • Helpful examples
                • Well-written

                Cons

                  Best Uses

                  • Intermediate
                  • Novice
                  • Student

                  Comments about oreilly Bioinformatics Data Skills:

                  It is a very good read for me. I am a wet biologist and I've been using linux commands for two years. but even so, I found some useful tricks. I really like the reproducible research part, the project organization part and documentation of your data and analysis part. To me, it is more important to learn these concepts. One good thing is that the author uses examples to illustrate the usage of the commands which is really helpful. Highly recommend for anyone who wants to do "good/reproducible" bioinformatics!
                  There are some minor grammar mistakes. Since it is an early release, it is totally understandable.

                  (5 of 5 customers found this review helpful)

                   
                  5.0

                  Great collection of practical tips

                  By Cosmin

                  from Paris, FR

                  About Me Bioinformatician, Scientist

                  Verified Reviewer

                  Pros

                  • Accurate
                  • Concise
                  • Easy to understand
                  • Helpful examples
                  • Well-written

                  Cons

                    Best Uses

                    • Intermediate

                    Comments about oreilly Bioinformatics Data Skills:

                    Many bioinformaticians are self-thaught and would definitely benefit a lot from a book like this one. It gathers together tons of practical advice, clearly explained. I especially liked the examples of how things can and will go wrong. The emphasis on reproducible data analysis is also welcome.

                    Displaying reviews 1-10

                    Back to top

                    Previous | Next »

                     
                    Buy 2 Get 1 Free Free Shipping Guarantee
                    Buying Options
                    Immediate Access - Go Digital what's this?
                    Ebook: $42.99
                    Formats:  ePub, Mobi, PDF
                    Print & Ebook: $54.99
                    Print: $49.99