book

Bioinformatics with Python Cookbook - Third Edition

Name: Bioinformatics with Python Cookbook - Third Edition
Author: Tiago Antao
ISBN: 9781803236421

by Tiago Antao

September 2022

Intermediate to advanced

360 pages

7h 37m

English

Packt Publishing

Read now

Unlock full access

Bioinformatics with Python Cookbook Third Edition
ContributorsAbout the authorAbout the reviewers
Preface
Who this book is forWhat this book coversTo get the most out of this bookDownload the example code filesDownload the color imagesConventions usedSectionsGetting readyHow to do it…How it works…There’s more…See alsoGet in touchReviewsShare Your Thoughts
Chapter 1: Python and the Surrounding Software Ecology
Installing the required basic software with AnacondaGetting readyHow to do it...There’s more...Installing the required software with DockerGetting readyHow to do it...See alsoInterfacing with R via rpy2Getting readyHow to do it...There’s more...See alsoPerforming R magic with JupyterGetting readyHow to do it...There’s more...See also
Chapter 2: Getting to Know NumPy, pandas, Arrow, and Matplotlib
Using pandas to process vaccine-adverse events Getting readyHow to do it...There’s more...See alsoDealing with the pitfalls of joining pandas DataFramesGetting readyHow to do it...There’s more...Reducing the memory usage of pandas DataFramesGetting readyHow to do it…See alsoAccelerating pandas processing with  Apache ArrowGetting readyHow to do it...There’s more...Understanding NumPy as the engine behind Python data science and bioinformaticsGetting readyHow to do it…See alsoIntroducing Matplotlib for chart generationGetting readyHow to do it...There’s more...See also
Chapter 3: Next-Generation Sequencing
Accessing GenBank and moving around NCBI databasesGetting readyHow to do it...There’s more...See alsoPerforming basic sequence analysisGetting readyHow to do it...There’s more...See alsoWorking with modern sequence formatsGetting readyHow to do it...There’s more...See alsoWorking with alignment dataGetting readyHow to do it...There’s more...See alsoExtracting data from VCF filesGetting readyHow to do it...There’s more...See alsoStudying genome accessibility and filtering SNP dataGetting readyHow to do it...There’s more...See alsoProcessing NGS data with HTSeqGetting readyHow to do it...There’s more...
Chapter 4: Advanced NGS Data Processing
Preparing a dataset for analysisGetting readyHow to do it…Using Mendelian error information for quality controlHow to do it…There’s more…Exploring the data with standard statisticsHow to do it…There’s more…Finding genomic features from sequencing annotationsHow to do it…There’s more…Doing metagenomics with QIIME 2 Python APIGetting readyHow to do it...There’s more...
Chapter 5: Working with Genomes
Technical requirementsWorking with high-quality reference genomesGetting readyHow to do it...There’s more...See alsoDealing with low-quality genome referencesGetting readyHow to do it...There’s more...See alsoTraversing genome annotationsGetting readyHow to do it...There’s more...See alsoExtracting genes from a reference using annotationsGetting readyHow to do it...There’s more...See alsoFinding orthologues with the Ensembl REST APIGetting readyHow to do it...There’s more...Retrieving gene ontology information from EnsemblGetting readyHow to do it...There’s more...See also
Chapter 6: Population Genetics
Managing datasets with PLINKGetting readyHow to do it...There’s more...See alsoUsing sgkit for population genetics analysis with xarrayGetting readyHow to do it...There’s more...Exploring a dataset with sgkitGetting readyHow to do it...There’s more...See alsoAnalyzing population structureGetting readyHow to do it...See alsoPerforming a PCAGetting readyHow to do it...There’s more...See alsoInvestigating population structure with admixtureGetting readyHow to do it...There’s more...
Chapter 7: Phylogenetics
Preparing a dataset for phylogenetic analysisGetting readyHow to do it...There’s more...See alsoAligning genetic and genomic dataGetting readyHow to do it...Comparing sequencesGetting readyHow to do it...There’s more...Reconstructing phylogenetic treesGetting readyHow to do it...There’s more...Playing recursively with treesGetting readyHow to do it...There’s more...Visualizing phylogenetic dataGetting readyHow to do it...There’s more...
Chapter 8: Using the Protein Data Bank
Finding a protein in multiple databasesGetting readyHow to do it...There’s moreIntroducing Bio.PDBGetting readyHow to do it...There’s moreExtracting more information from a PDB fileGetting readyHow to do it...Computing molecular distances on a PDB fileGetting readyHow to do it...Performing geometric operationsGetting readyHow to do it...There’s moreAnimating with PyMOLGetting readyHow to do it...There’s moreParsing mmCIF files using BiopythonGetting readyHow to do it...There’s more

Chapter 9: Bioinformatics Pipelines
Introducing Galaxy serversGetting readyHow to do it…There’s moreAccessing Galaxy using the APIGetting readyHow to do it…Deploying a variant analysis pipeline with SnakemakeGetting readyHow to do it…There’s moreDeploying a variant analysis pipeline with NextflowGetting readyHow to do it…There’s more
Chapter 10: Machine Learning for Bioinformatics
Introducing scikit-learn with a PCA exampleGetting readyHow to do it...There’s more...Using clustering over PCA to classify samplesGetting readyHow to do it...There’s more...Exploring breast cancer traits using Decision TreesGetting readyHow to do it...Predicting breast cancer outcomes using Random Forests Getting readyHow to do it…There’s more...
Chapter 11: Parallel Processing with Dask and Zarr
Reading genomics data with Zarr Getting readyHow to do it...There’s more...See alsoParallel processing of data using Python multiprocessingGetting readyHow to do it...There’s more...See alsoUsing Dask to process genomic data based on NumPy arraysGetting readyHow to do it...There’s more...See alsoScheduling tasks with dask.distributedGetting readyHow to do it...There’s more...See also
Chapter 12: Functional Programming for Bioinformatics
Understanding pure functions Getting readyHow to do it...There’s more...Understanding immutabilityGetting readyHow to do it...There’s more...Avoiding mutability as a robust development patternGetting readyHow to do it...There’s more...Using lazy programming for pipeliningGetting readyHow to do it...There’s more...The limits of recursion with PythonGetting readyHow to do it...There’s more...A showcase of Python’s functools moduleGetting readyHow to do it...There’s more...See also...
Index
Why subscribe?
Other Books You May EnjoyPackt is searching for authors like youShare Your Thoughts

Overview

Learn how to leverage Python's powerful libraries and tools to tackle complex bioinformatics challenges with the 'Bioinformatics with Python Cookbook'. This hands-on guide equips you to analyze biological data, develop bioinformatics pipelines, and apply machine learning techniques to solve real-world problems in computational biology.

What this Book will help me do

Master the use of Python data processing libraries like NumPy and pandas for biological data analysis.
Build and automate bioinformatics pipelines with Galaxy servers and Snakemake.
Implement solutions for genomic data analysis, from next-generation sequencing to proteomics.
Apply statistical and machine learning techniques using tools like scikit-learn to bioinformatics datasets.
Perform efficient data analysis with parallel processing frameworks such as Dask.

Author(s)

Tiago Antao, a computational biologist and software developer, brings years of expertise in bioinformatics and Python programming to this book. His hands-on teaching methodology and real-world examples simplify complex topics, making computational biology accessible and practical for a broad audience. Through his work, Tiago emphasizes modern and scalable programming techniques.

Who is it for?

This book is ideal for computational biologists, bioinformatics researchers, data scientists, and Python developers who aim to advance their knowledge in analyzing biological datasets. Readers should have a foundational understanding of Python and computational methods, alongside a basic grasp of biological concepts, to fully benefit from the material presented.

Become an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
and much more.

Read now

Unlock full access

More than 5,000 organizations count on O’Reilly

O’Reilly covers everything we've got, with content to help us build a world-class technology community, upgrade the capabilities and competencies of our teams, and improve overall team performance as well as their engagement.

Julian F.

Head of Cybersecurity

I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.

Addison B.

Field Engineer

I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.

Amir M.

Data Platform Tech Lead

I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.

Mark W.

Embedded Software Engineer

Publisher Resources

ISBN: 9781803236421

Cloud Computing

Data Engineering

Data Science

AI & ML

Programming Languages

Software Architecture

IT/Ops

Security

Design

Business

Soft Skills