Bioinformatics With Python Cookbook

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Bioinformatics With Python Cookbook

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Author : Tiago Antao
language : en
Publisher: Packt Publishing Ltd
Release Date : 2022-09-27

Bioinformatics With Python Cookbook written by Tiago Antao and has been published by Packt Publishing Ltd this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-09-27 with Computers categories.

Discover modern, next-generation sequencing libraries from the powerful Python ecosystem to perform cutting-edge research and analyze large amounts of biological data Key Features Perform complex bioinformatics analysis using the most essential Python libraries and applications Implement next-generation sequencing, metagenomics, automating analysis, population genetics, and much more Explore various statistical and machine learning techniques for bioinformatics data analysis Book Description Bioinformatics is an active research field that uses a range of simple-to-advanced computations to extract valuable information from biological data, and this book will show you how to manage these tasks using Python. This updated third edition of the Bioinformatics with Python Cookbook begins with a quick overview of the various tools and libraries in the Python ecosystem that will help you convert, analyze, and visualize biological datasets. Next, you'll cover key techniques for next-generation sequencing, single-cell analysis, genomics, metagenomics, population genetics, phylogenetics, and proteomics with the help of real-world examples. You'll learn how to work with important pipeline systems, such as Galaxy servers and Snakemake, and understand the various modules in Python for functional and asynchronous programming. This book will also help you explore topics such as SNP discovery using statistical approaches under high-performance computing frameworks, including Dask and Spark. In addition to this, you'll explore the application of machine learning algorithms in bioinformatics. By the end of this bioinformatics Python book, you'll be equipped with the knowledge you need to implement the latest programming techniques and frameworks, empowering you to deal with bioinformatics data on every scale. What you will learn Become well-versed with data processing libraries such as NumPy, pandas, arrow, and zarr in the context of bioinformatic analysis Interact with genomic databases Solve real-world problems in the fields of population genetics, phylogenetics, and proteomics Build bioinformatics pipelines using a Galaxy server and Snakemake Work with functools and itertools for functional programming Perform parallel processing with Dask on biological data Explore principal component analysis (PCA) techniques with scikit-learn Who this book is for This book is for bioinformatics analysts, data scientists, computational biologists, researchers, and Python developers who want to address intermediate-to-advanced biological and bioinformatics problems. Working knowledge of the Python programming language is expected. Basic knowledge of biology will also be helpful.

Bioinformatics With Python Cookbook

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Author : Tiago Antao
language : en
Publisher: Packt Publishing Ltd
Release Date : 2018-11-30

Bioinformatics With Python Cookbook written by Tiago Antao and has been published by Packt Publishing Ltd this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-11-30 with Computers categories.

Discover modern, next-generation sequencing libraries from Python ecosystem to analyze large amounts of biological data Key Features Perform complex bioinformatics analysis using the most important Python libraries and applications Implement next-generation sequencing, metagenomics, automating analysis, population genetics, and more Explore various statistical and machine learning techniques for bioinformatics data analysis Book Description 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 will help you get a better understanding of working with a Galaxy server, which is the most widely used bioinformatics web-based pipeline system. This updated edition also includes advanced next-generation sequencing filtering techniques. You'll also explore topics such as SNP discovery using statistical approaches under high-performance computing frameworks such as Dask and Spark. By the end of this book, you'll be able to use and implement modern programming techniques and frameworks to deal with the ever-increasing deluge of bioinformatics data. What you will learn 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 Use High-performance computing techniques with Dask and Spark Visualize protein dataset interactions using Cytoscape Use PCA and Decision Trees, two machine learning techniques, with biological datasets Who this book is for This book is for Data data Scientistsscientists, Bioinformatics 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.

Bioinformatics With Python Cookbook

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Author : Shane Brubaker
language : en
Publisher: Packt Publishing Ltd
Release Date : 2025-12-19

Bioinformatics With Python Cookbook written by Shane Brubaker and has been published by Packt Publishing Ltd this book supported file pdf, txt, epub, kindle and other format this book has been release on 2025-12-19 with Computers categories.

Enhance your bioinformatics toolbox with practical Python recipes, tips, and tricks for key tasks like aligning sequence data, calling variants, and building Infrastructure as Code Key Features Perform sequence analysis at primary, secondary, and tertiary levels using Python libraries Solve real-world problems in the fields of phylogenetics, protein design, and annotation Use language models and other AI techniques to work with multimodal bioinformatics data Purchase of the print or Kindle book includes a free PDF eBook Book DescriptionIf you've ever felt overwhelmed by the vast number of Python tools available for bioinformatics, you're not alone. The Bioinformatics with Python Cookbook is a recipe-based guide that explores practical approaches for solving classic bioinformatics challenges, showing you which Python packages work best for each task. You’ll start with the essential Python libraries for data science and bioinformatics, then move through key workflows in sequencing analysis, quality control, alignment, and variant calling. Along the way, you’ll pick up modern coding practices, explore recent advances in bioinformatics research, and gain hands-on experience with libraries such as NumPy, pandas, and sci-kit learn. This book walks you through core bioinformatics tasks such as phylogenetic analysis and population genomics while familiarizing you with the wealth of modern public bioinformatics databases. You’ll learn cloud computing approaches used by researchers, set up workflow orchestration systems for controlling bioinformatics pipelines, and see how AI and the use of large language models (LLMs) are reshaping the field–right down to designing proteins and DNA. By the end of this book, you’ll be ready to apply Python for real bioinformatics work and launch bioinformatics pipelines for your research.What you will learn Process, analyze, and align sequencing data Call variants and interpret their biological meaning Use modern cloud infrastructure to launch bioinformatics workflows Ingest, clean, and transform data efficiently Explore how AI is shaping the future of bioinformatics Leverage imaging data for biological insights Apply single-cell sequencing to cluster and compare gene expression Who this book is for This book is for early- to mid-level practitioners in bioinformatics, data science, and software engineering who want to improve their skills and apply practical solutions to real-world problems. You should have a basic understanding of biology, including DNA, proteins, and cell structure, as well as Python programming and software engineering techniques. While prior exposure to machine learning with Python is not essential, experience with a cloud computing platform (AWS, GCP, or Azure) will be helpful.

Bioinformatics With Python Cookbook

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Author : Tiago Antao
language : en
Publisher: Packt Publishing Ltd
Release Date : 2015-06-25

Bioinformatics With Python Cookbook written by Tiago Antao and has been published by Packt Publishing Ltd this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-06-25 with Computers categories.

If you are either a computational biologist or a Python programmer, you will probably relate to the expression "explosive growth, exciting times". Python is arguably the main programming language for big data, and the deluge of data in biology, mostly from genomics and proteomics, makes bioinformatics one of the most exciting fields in data science. Using the hands-on recipes in this book, you'll be able to do practical research and analysis in computational biology with Python. We cover modern, next-generation sequencing libraries and explore real-world examples on how to handle real data. The main focus of the book is the practical application of bioinformatics, but we also cover modern programming techniques and frameworks to deal with the ever increasing deluge of bioinformatics data.

Bioinformatics With Python Cookbook Second Edition

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Author : Tiago Antao
language : en
Publisher:
Release Date : 2018

Bioinformatics With Python Cookbook Second Edition written by Tiago Antao and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018 with categories.

Discover modern, next-generation sequencing libraries from Python ecosystem to analyze large amounts of biological data Key Features Perform complex bioinformatics analysis using the most important Python libraries and applications Implement next-generation sequencing, metagenomics, automating analysis, population genetics, and more Explore various statistical and machine learning techniques for bioinformatics data analysis Book Description 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 will help you get a better understanding of working with a Galaxy server, which is the most widely used bioinformatics web-based pipeline system. This updated edition also includes advanced next-generation sequencing filtering techniques. You'll also explore topics such as SNP discovery using statistical approaches under high-performance computing frameworks such as Dask and Spark. By the end of this book, you'll be able to use and implement modern programming techniques and frameworks to deal with the ever-increasing deluge of bioinformatics data. What you will learn 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 Use High-performance computing techniques with Dask and Spark Visualize protein dataset interactions using Cytoscape Use PCA and Decision Trees, two machine learning techniques, with biological datasets Who this book is for This book is for Data data Scientistsscientists, Bioinformatics 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. Downloading the example code for this book You can download the example code files for all Packt books you have purchased from your account at http://w ...

R Bioinformatics Cookbook

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Author : Dan MacLean
language : en
Publisher:
Release Date : 2019-10-11

R Bioinformatics Cookbook written by Dan MacLean and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-10-11 with Computers categories.

Over 60 recipes to model and handle real-life biological data using modern libraries from the R ecosystem Key Features Apply modern R packages to handle biological data using real-world examples Represent biological data with advanced visualizations suitable for research and publications Handle real-world problems in bioinformatics such as next-generation sequencing, metagenomics, and automating analyses Book Description Handling biological data effectively requires an in-depth knowledge of machine learning techniques and computational skills, along with an understanding of how to use tools such as edgeR and DESeq. With the R Bioinformatics Cookbook, you'll explore all this and more, tackling common and not-so-common challenges in the bioinformatics domain using real-world examples. This book will use a recipe-based approach to show you how to perform practical research and analysis in computational biology with R. You will learn how to effectively analyze your data with the latest tools in Bioconductor, ggplot, and tidyverse. The book will guide you through the essential tools in Bioconductor to help you understand and carry out protocols in RNAseq, phylogenetics, genomics, and sequence analysis. As you progress, you will get up to speed with how machine learning techniques can be used in the bioinformatics domain. You will gradually develop key computational skills such as creating reusable workflows in R Markdown and packages for code reuse. By the end of this book, you'll have gained a solid understanding of the most important and widely used techniques in bioinformatic analysis and the tools you need to work with real biological data. What you will learn Employ Bioconductor to determine differential expressions in RNAseq data Run SAMtools and develop pipelines to find single nucleotide polymorphisms (SNPs) and Indels Use ggplot to create and annotate a range of visualizations Query external databases with Ensembl to find functional genomics information Execute large-scale multiple sequence alignment with DECIPHER to perform comparative genomics Use d3.js and Plotly to create dynamic and interactive web graphics Use k-nearest neighbors, support vector machines and random forests to find groups and classify data Who this book is for This book is for bioinformaticians, data analysts, researchers, and R developers who want to address intermediate-to-advanced biological and bioinformatics problems by learning through a recipe-based approach. Working knowledge of R programming language and basic knowledge of bioinformatics are prerequisites.

R Bioinformatics Cookbook Second Edition

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Author : Dan Maclean
language : en
Publisher:
Release Date : 2023-10-31

R Bioinformatics Cookbook Second Edition written by Dan Maclean and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-10-31 with categories.

This book takes a unique problem-solution approach to handling complex tasks in the bioinformatics domain using different datasets present in the book.

Python Machine Learning Cookbook

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Author : Giuseppe Ciaburro
language : en
Publisher: Packt Publishing Ltd
Release Date : 2019-03-30

Python Machine Learning Cookbook written by Giuseppe Ciaburro and has been published by Packt Publishing Ltd this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-03-30 with Computers categories.

Discover powerful ways to effectively solve real-world machine learning problems using key libraries including scikit-learn, TensorFlow, and PyTorch Key FeaturesLearn and implement machine learning algorithms in a variety of real-life scenariosCover a range of tasks catering to supervised, unsupervised and reinforcement learning techniquesFind easy-to-follow code solutions for tackling common and not-so-common challengesBook Description This eagerly anticipated second edition of the popular Python Machine Learning Cookbook will enable you to adopt a fresh approach to dealing with real-world machine learning and deep learning tasks. With the help of over 100 recipes, you will learn to build powerful machine learning applications using modern libraries from the Python ecosystem. The book will also guide you on how to implement various machine learning algorithms for classification, clustering, and recommendation engines, using a recipe-based approach. With emphasis on practical solutions, dedicated sections in the book will help you to apply supervised and unsupervised learning techniques to real-world problems. Toward the concluding chapters, you will get to grips with recipes that teach you advanced techniques including reinforcement learning, deep neural networks, and automated machine learning. By the end of this book, you will be equipped with the skills you need to apply machine learning techniques and leverage the full capabilities of the Python ecosystem through real-world examples. What you will learnUse predictive modeling and apply it to real-world problemsExplore data visualization techniques to interact with your dataLearn how to build a recommendation engineUnderstand how to interact with text data and build models to analyze itWork with speech data and recognize spoken words using Hidden Markov ModelsGet well versed with reinforcement learning, automated ML, and transfer learningWork with image data and build systems for image recognition and biometric face recognitionUse deep neural networks to build an optical character recognition systemWho this book is for This book is for data scientists, machine learning developers, deep learning enthusiasts and Python programmers who want to solve real-world challenges using machine-learning techniques and algorithms. If you are facing challenges at work and want ready-to-use code solutions to cover key tasks in machine learning and the deep learning domain, then this book is what you need. Familiarity with Python programming and machine learning concepts will be useful.

Containerisation And Multimodal Transport In India

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Author : K. V. Hariharan
language : en
Publisher:
Release Date : 2003

Containerisation And Multimodal Transport In India written by K. V. Hariharan and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2003 with Containerization categories.

Bioinformatics Programming Using Python

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Author : Mitchell L Model
language : en
Publisher:
Release Date : 2010

Bioinformatics Programming Using Python written by Mitchell L Model and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with categories.