Bioinformatics With Python Cookbook

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Bioinformatics with Python Cookbook

Tiago Antao
Bioinformatics with Python Cookbook Book PDF

Author : Tiago Antao
Publisher : Packt Publishing Ltd
Page : 352 pages
File Size : 50,7 Mb
Release : 2018-11-30
Category : Computers
ISBN : 9781789349986

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Bioinformatics with Python Cookbook by Tiago Antao Pdf

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

Tiago Antao
Bioinformatics with Python Cookbook Book PDF

Author : Tiago Antao
Publisher : Packt Publishing Ltd
Page : 306 pages
File Size : 54,9 Mb
Release : 2015-06-25
Category : Computers
ISBN : 9781783558650

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Bioinformatics with Python Cookbook by Tiago Antao Pdf

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

Tiago Antao
Bioinformatics with Python Cookbook Book PDF

Author : Tiago Antao
Publisher : Packt Publishing Ltd
Page : 360 pages
File Size : 46,6 Mb
Release : 2022-09-27
Category : Computers
ISBN : 9781803247724

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Bioinformatics with Python Cookbook by Tiago Antao Pdf

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.

R Bioinformatics Cookbook

Dan MacLean
R Bioinformatics Cookbook Book PDF

Author : Dan MacLean
Publisher : Packt Publishing Ltd
Page : 307 pages
File Size : 50,7 Mb
Release : 2019-10-11
Category : Science
ISBN : 9781789955590

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R Bioinformatics Cookbook by Dan MacLean Pdf

Over 60 recipes to model and handle real-life biological data using modern libraries from the R ecosystem Key FeaturesApply modern R packages to handle biological data using real-world examplesRepresent biological data with advanced visualizations suitable for research and publicationsHandle real-world problems in bioinformatics such as next-generation sequencing, metagenomics, and automating analysesBook 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 learnEmploy Bioconductor to determine differential expressions in RNAseq dataRun SAMtools and develop pipelines to find single nucleotide polymorphisms (SNPs) and IndelsUse ggplot to create and annotate a range of visualizationsQuery external databases with Ensembl to find functional genomics informationExecute large-scale multiple sequence alignment with DECIPHER to perform comparative genomicsUse d3.js and Plotly to create dynamic and interactive web graphicsUse k-nearest neighbors, support vector machines and random forests to find groups and classify dataWho 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.

Mastering Python for Bioinformatics

Ken Youens-Clark
Mastering Python for Bioinformatics Book PDF

Author : Ken Youens-Clark
Publisher : "O'Reilly Media, Inc."
Page : 457 pages
File Size : 40,8 Mb
Release : 2021-05-05
Category : Computers
ISBN : 9781098100858

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Mastering Python for Bioinformatics by Ken Youens-Clark Pdf

Life scientists today urgently need training in bioinformatics skills. Too many bioinformatics programs are poorly written and barely maintained--usually by students and researchers who've never learned basic programming skills. This practical guide shows postdoc bioinformatics professionals and students how to exploit the best parts of Python to solve problems in biology while creating documented, tested, reproducible software. Ken Youens-Clark, author of Tiny Python Projects (Manning), demonstrates not only how to write effective Python code but also how to use tests to write and refactor scientific programs. You'll learn the latest Python features and toolsâ??including linters, formatters, type checkers, and testsâ??to create documented and tested programs. You'll also tackle 14 challenges in Rosalind, a problem-solving platform for learning bioinformatics and programming. Create command-line Python programs to document and validate parameters Write tests to verify refactor programs and confirm they're correct Address bioinformatics ideas using Python data structures and modules such as Biopython Create reproducible shortcuts and workflows using makefiles Parse essential bioinformatics file formats such as FASTA and FASTQ Find patterns of text using regular expressions Use higher-order functions in Python like filter(), map(), and reduce()

Bioinformatics Programming Using Python

Mitchell L Model
Bioinformatics Programming Using Python Book PDF

Author : Mitchell L Model
Publisher : "O'Reilly Media, Inc."
Page : 526 pages
File Size : 52,9 Mb
Release : 2009-12-08
Category : Science
ISBN : 9781449382902

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Bioinformatics Programming Using Python by Mitchell L Model Pdf

Powerful, flexible, and easy to use, Python is an ideal language for building software tools and applications for life science research and development. This unique book shows you how to program with Python, using code examples taken directly from bioinformatics. In a short time, you'll be using sophisticated techniques and Python modules that are particularly effective for bioinformatics programming. Bioinformatics Programming Using Python is perfect for anyone involved with bioinformatics -- researchers, support staff, students, and software developers interested in writing bioinformatics applications. You'll find it useful whether you already use Python, write code in another language, or have no programming experience at all. It's an excellent self-instruction tool, as well as a handy reference when facing the challenges of real-life programming tasks. Become familiar with Python's fundamentals, including ways to develop simple applications Learn how to use Python modules for pattern matching, structured text processing, online data retrieval, and database access Discover generalized patterns that cover a large proportion of how Python code is used in bioinformatics Learn how to apply the principles and techniques of object-oriented programming Benefit from the "tips and traps" section in each chapter

Bioinformatics Data Skills

Vince Buffalo
Bioinformatics Data Skills Book PDF

Author : Vince Buffalo
Publisher : "O'Reilly Media, Inc."
Page : 538 pages
File Size : 42,8 Mb
Release : 2015-07
Category : Computers
ISBN : 9781449367510

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Bioinformatics Data Skills by Vince Buffalo Pdf

Learn the data skills necessary for turning large sequencing datasets into reproducible and robust biological findings. With this practical guide, youâ??ll learn how to use freely available open source tools to extract meaning from large complex biological data sets. At no other point in human history has our ability to understand lifeâ??s complexities been so dependent on our skills to work with and analyze data. This intermediate-level book teaches the general computational and data skills you need to analyze biological data. If you have experience with a scripting language like Python, youâ??re ready to get started. Go from handling small problems with messy scripts to tackling large problems with clever methods and tools Process bioinformatics data with powerful Unix pipelines and data tools Learn how to use exploratory data analysis techniques in the R language Use efficient methods to work with genomic range data and range operations Work with common genomics data file formats like FASTA, FASTQ, SAM, and BAM Manage your bioinformatics project with the Git version control system Tackle tedious data processing tasks with with Bash scripts and Makefiles

Bioinformatics Algorithms

Miguel Rocha,Pedro G. Ferreira
Bioinformatics Algorithms Book PDF

Author : Miguel Rocha,Pedro G. Ferreira
Publisher : Academic Press
Page : 402 pages
File Size : 43,8 Mb
Release : 2018-06-08
Category : Technology & Engineering
ISBN : 9780128125212

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Bioinformatics Algorithms by Miguel Rocha,Pedro G. Ferreira Pdf

Bioinformatics Algorithms: Design and Implementation in Python provides a comprehensive book on many of the most important bioinformatics problems, putting forward the best algorithms and showing how to implement them. The book focuses on the use of the Python programming language and its algorithms, which is quickly becoming the most popular language in the bioinformatics field. Readers will find the tools they need to improve their knowledge and skills with regard to algorithm development and implementation, and will also uncover prototypes of bioinformatics applications that demonstrate the main principles underlying real world applications. Presents an ideal text for bioinformatics students with little to no knowledge of computer programming Based on over 12 years of pedagogical materials used by the authors in their own classrooms Features a companion website with downloadable codes and runnable examples (such as using Jupyter Notebooks) and exercises relating to the book

Python for Bioinformatics

Jason Kinser
Python for Bioinformatics Book PDF

Author : Jason Kinser
Publisher : Jones & Bartlett Publishers
Page : 436 pages
File Size : 41,8 Mb
Release : 2010-10-25
Category : Computers
ISBN : 9781449613075

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Python for Bioinformatics by Jason Kinser Pdf

Python for Bioinformatics provides a clear introduction to the Python programming language and instructs beginners on the development of simple programming exercises. Important Notice: The digital edition of this book is missing some of the images or content found in the physical edition.

Python for Bioinformatics

Sebastian Bassi
Python for Bioinformatics Book PDF

Author : Sebastian Bassi
Publisher : CRC Press
Page : 510 pages
File Size : 55,7 Mb
Release : 2017-08-07
Category : Mathematics
ISBN : 9781351976954

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Python for Bioinformatics by Sebastian Bassi Pdf

In today's data driven biology, programming knowledge is essential in turning ideas into testable hypothesis. Based on the author’s extensive experience, Python for Bioinformatics, Second Edition helps biologists get to grips with the basics of software development. Requiring no prior knowledge of programming-related concepts, the book focuses on the easy-to-use, yet powerful, Python computer language. This new edition is updated throughout to Python 3 and is designed not just to help scientists master the basics, but to do more in less time and in a reproducible way. New developments added in this edition include NoSQL databases, the Anaconda Python distribution, graphical libraries like Bokeh, and the use of Github for collaborative development.

Managing Your Biological Data with Python

Allegra Via,Kristian Rother,Anna Tramontano
Managing Your Biological Data with Python Book PDF

Author : Allegra Via,Kristian Rother,Anna Tramontano
Publisher : CRC Press
Page : 560 pages
File Size : 44,8 Mb
Release : 2014-03-18
Category : Computers
ISBN : 9781439880944

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Managing Your Biological Data with Python by Allegra Via,Kristian Rother,Anna Tramontano Pdf

Take Control of Your Data and Use Python with ConfidenceRequiring no prior programming experience, Managing Your Biological Data with Python empowers biologists and other life scientists to work with biological data on their own using the Python language. The book teaches them not only how to program but also how to manage their data. It shows how

Python for Biologists

Martin Jones
Python for Biologists Book PDF

Author : Martin Jones
Publisher : Createspace Independent Publishing Platform
Page : 248 pages
File Size : 43,8 Mb
Release : 2013
Category : Biology
ISBN : UCR:31210023746751

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Python for Biologists by Martin Jones Pdf

Python for biologists is a complete programming course for beginners that will give you the skills you need to tackle common biological and bioinformatics problems.

Practical Data Science Cookbook

Prabhanjan Tattar,Tony Ojeda,Sean Patrick Murphy,Benjamin Bengfort,Abhijit Dasgupta
Practical Data Science Cookbook Book PDF

Author : Prabhanjan Tattar,Tony Ojeda,Sean Patrick Murphy,Benjamin Bengfort,Abhijit Dasgupta
Publisher : Packt Publishing Ltd
Page : 428 pages
File Size : 41,7 Mb
Release : 2017-06-29
Category : Computers
ISBN : 9781787123267

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Practical Data Science Cookbook by Prabhanjan Tattar,Tony Ojeda,Sean Patrick Murphy,Benjamin Bengfort,Abhijit Dasgupta Pdf

Over 85 recipes to help you complete real-world data science projects in R and Python About This Book Tackle every step in the data science pipeline and use it to acquire, clean, analyze, and visualize your data Get beyond the theory and implement real-world projects in data science using R and Python Easy-to-follow recipes will help you understand and implement the numerical computing concepts Who This Book Is For If you are an aspiring data scientist who wants to learn data science and numerical programming concepts through hands-on, real-world project examples, this is the book for you. Whether you are brand new to data science or you are a seasoned expert, you will benefit from learning about the structure of real-world data science projects and the programming examples in R and Python. What You Will Learn Learn and understand the installation procedure and environment required for R and Python on various platforms Prepare data for analysis by implement various data science concepts such as acquisition, cleaning and munging through R and Python Build a predictive model and an exploratory model Analyze the results of your model and create reports on the acquired data Build various tree-based methods and Build random forest In Detail As increasing amounts of data are generated each year, the need to analyze and create value out of it is more important than ever. Companies that know what to do with their data and how to do it well will have a competitive advantage over companies that don't. Because of this, there will be an increasing demand for people that possess both the analytical and technical abilities to extract valuable insights from data and create valuable solutions that put those insights to use. Starting with the basics, this book covers how to set up your numerical programming environment, introduces you to the data science pipeline, and guides you through several data projects in a step-by-step format. By sequentially working through the steps in each chapter, you will quickly familiarize yourself with the process and learn how to apply it to a variety of situations with examples using the two most popular programming languages for data analysis—R and Python. Style and approach This step-by-step guide to data science is full of hands-on examples of real-world data science tasks. Each recipe focuses on a particular task involved in the data science pipeline, ranging from readying the dataset to analytics and visualization

Programming Collective Intelligence

Toby Segaran
Programming Collective Intelligence Book PDF

Author : Toby Segaran
Publisher : "O'Reilly Media, Inc."
Page : 361 pages
File Size : 42,6 Mb
Release : 2007-08-16
Category : Computers
ISBN : 9780596550684

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Programming Collective Intelligence by Toby Segaran Pdf

Want to tap the power behind search rankings, product recommendations, social bookmarking, and online matchmaking? This fascinating book demonstrates how you can build Web 2.0 applications to mine the enormous amount of data created by people on the Internet. With the sophisticated algorithms in this book, you can write smart programs to access interesting datasets from other web sites, collect data from users of your own applications, and analyze and understand the data once you've found it. Programming Collective Intelligence takes you into the world of machine learning and statistics, and explains how to draw conclusions about user experience, marketing, personal tastes, and human behavior in general -- all from information that you and others collect every day. Each algorithm is described clearly and concisely with code that can immediately be used on your web site, blog, Wiki, or specialized application. This book explains: Collaborative filtering techniques that enable online retailers to recommend products or media Methods of clustering to detect groups of similar items in a large dataset Search engine features -- crawlers, indexers, query engines, and the PageRank algorithm Optimization algorithms that search millions of possible solutions to a problem and choose the best one Bayesian filtering, used in spam filters for classifying documents based on word types and other features Using decision trees not only to make predictions, but to model the way decisions are made Predicting numerical values rather than classifications to build price models Support vector machines to match people in online dating sites Non-negative matrix factorization to find the independent features in a dataset Evolving intelligence for problem solving -- how a computer develops its skill by improving its own code the more it plays a game Each chapter includes exercises for extending the algorithms to make them more powerful. Go beyond simple database-backed applications and put the wealth of Internet data to work for you. "Bravo! I cannot think of a better way for a developer to first learn these algorithms and methods, nor can I think of a better way for me (an old AI dog) to reinvigorate my knowledge of the details." -- Dan Russell, Google "Toby's book does a great job of breaking down the complex subject matter of machine-learning algorithms into practical, easy-to-understand examples that can be directly applied to analysis of social interaction across the Web today. If I had this book two years ago, it would have saved precious time going down some fruitless paths." -- Tim Wolters, CTO, Collective Intellect

R Cookbook

JD Long,Paul Teetor
R Cookbook Book PDF

Author : JD Long,Paul Teetor
Publisher : "O'Reilly Media, Inc."
Page : 600 pages
File Size : 46,5 Mb
Release : 2019-06-21
Category : Computers
ISBN : 9781492040637

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R Cookbook by JD Long,Paul Teetor Pdf

Perform data analysis with R quickly and efficiently with more than 275 practical recipes in this expanded second edition. The R language provides everything you need to do statistical work, but its structure can be difficult to master. These task-oriented recipes make you productive with R immediately. Solutions range from basic tasks to input and output, general statistics, graphics, and linear regression. Each recipe addresses a specific problem and includes a discussion that explains the solution and provides insight into how it works. If you’re a beginner, R Cookbook will help get you started. If you’re an intermediate user, this book will jog your memory and expand your horizons. You’ll get the job done faster and learn more about R in the process. Create vectors, handle variables, and perform basic functions Simplify data input and output Tackle data structures such as matrices, lists, factors, and data frames Work with probability, probability distributions, and random variables Calculate statistics and confidence intervals and perform statistical tests Create a variety of graphic displays Build statistical models with linear regressions and analysis of variance (ANOVA) Explore advanced statistical techniques, such as finding clusters in your data