This is the code repository for Bioinformatics with Python Cookbook, Second Edition, published by Packt.
Learn how to use modern Python bioinformatics libraries and applications to do cutting-edge research in computational biology
Bioinformatics is an active research field that uses a range of simple-to-advanced computations to extract valuable information from biological data. This book covers next-generation sequencing, genomics, metagenomics, population genetics, phylogenetics, and proteomics. You'll learn modern programming techniques to analyze large amounts of biological data. With the help of real-world examples, you'll convert, analyze, and visualize datasets using various Python tools and libraries.
This book covers the following exciting features:
- Learn how to process large next-generation sequencing (NGS) datasets
- Work with genomic dataset using the FASTQ, BAM, and VCF formats
- Learn to perform sequence comparison and phylogenetic reconstruction
- Perform complex analysis with protemics data
- Use Python to interact with Galaxy servers
If you feel this book is for you, get your copy today!
All of the code is organized into folders. For example, Chapter02.
The code will look like the following:
import os
from IPython.display import Image
import rpy2.robjects as robjects
import pandas as pd
from rpy2.robjects import pandas2ri
Following is what you need for this book: This book is for data scientists, bioinformatics analysts, researchers, and Python developers who want to address intermediate-to-advanced biological and bioinformatics problems using a recipe-based approach. Working knowledge of the Python programming language is expected.
With the following software and hardware list you can run all code files present in the book (Chapter 1-11).
| Chapter | Software required | OS required |
|---|---|---|
| 1-11 | Python, Jupyter Notebook | Windows, Mac OS X, and Linux (Any) |
We also provide a PDF file that has color images of the screenshots/diagrams used in this book. Click here to download it.
Tiago Antao is a bioinformatician currently working in the field of genomics. He was originally a computer scientist but he crossed over to computational biology with an MSc in Bioinformatics from the Faculty of Sciences at the University of Porto, Portugal, and a PhD on the spread of drug-resistant malaria from the Liverpool School of Tropical Medicine in the UK. He is one of the co-authors of Biopython, a major bioinformatics package written in Python. In his post-doctoral career, he has worked with human datasets at the University of Cambridge (UK) and with mosquito whole genome sequence data at the University of Oxford (UK). He is currently working as a research scientist at the University of Montana.
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