June 2015
Intermediate to advanced
306 pages
6h 50m
English
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Chapter 1. Python and the Surrounding Software Ecology
In this chapter, we will cover the following recipes:
- Installing the required software with Anaconda
- Installing the required software with Docker
- Interfacing with R via rpy2
- Performing R magic with IPython
Introduction
We will start by installing the required software. This will include the Python distribution, some fundamental Python libraries, and external bioinformatics software. Here, we will also be concerned with the world outside Python. In bioinformatics and Big Data, R is also a major player; therefore, you will learn how to interact with it via rpy2 a Python/R bridge. We will also explore the advantages that the IPython framework can give us in order to efficiently interface with R. This ...