New PDF release: Bioinformatics Data Skills: Reproducible and Robust Research

By Vince Buffalo

ISBN-10: 1449367372

ISBN-13: 9781449367374

This sensible ebook teaches the abilities that scientists want for turning huge sequencing datasets into reproducible and powerful organic findings. Many biologists start their bioinformatics education by means of studying scripting languages like Python and R along the Unix command line. yet there's a big hole among realizing a number of programming languages and being ready to investigate quite a lot of organic data.
Rather than train bioinformatics as a collection of workflows which are prone to switch with this quickly evolving box, this publication demsonstrates the perform of bioinformatics via information abilities. Rigorous evaluate of knowledge caliber and of the effectiveness of instruments is the root of reproducible and powerful bioinformatics research. via open resource and freely on hand instruments, you'll research not just the way to do bioinformatics, yet the way to process difficulties as a bioinformatician.
Go from dealing with small issues of messy scripts to tackling huge issues of shrewdpermanent tools and tools
Focus on high-throughput (or "next generation") sequencing data
Learn information research with smooth tools, as opposed to overlaying older theoretical concepts
Understand how you can opt for and enforce the easiest instrument for the job
Delve into tools that result in more uncomplicated, extra reproducible, and strong bioinformatics research

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Extra info for Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools (1st Edition)

Example text

Next, we need to consider whether, by allowing zero values for dates, we are also making our x axis substantially longer (my count query yielded 1211 rows, but there are a total of 1822 days in the range specified, which is 1998-2002). Maybe showing zero count days might not work; if the graph is so crowded, we cannot see the gaps anyway. To compare, we can quickly run the same data into Google Spreadsheets (you can do this in Excel or D3 too), but this time, we will only select our count column to build the graph, thereby forcing Google Spreadsheets to not show dates on the x axis.

Yet, there are still some options that can differentiate one delimited format from another. The first differentiator is how each instance of the data (each row) is separated. Usually at the end of a line, a new line, or a carriage return, or both are used depending on the operating environment in use during the creation of the file. Seeing invisible characters In the preceding example, the new line or carriage return is invisible. How do you see the invisible characters? We will read the same file in Text Wrangler on a Mac (similar full-featured editors such as Notepad++ are available for Windows), where we can use the Show invisibles option (located by navigating to View | Text Display).

Type conversion at the SQL level Here, we will walk through a few common cases when SQL can be used to manipulate data types. Example one – parsing MySQL date into a formatted string For this example, we will return to the Enron e-mail dataset we used in Chapter 1, Why Do You Need Clean Data?. As with the previous example, we are going to look in the message table, where we have been using the date column, which is stored as a datetime MySQL data type. Suppose we want to print a full date with spelled-out months (as opposed to numbers) and even the day of the week and time of day.

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Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools (1st Edition) by Vince Buffalo


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