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Bioinformatics with Python Cookbook

You're reading from   Bioinformatics with Python Cookbook Use modern Python libraries and applications to solve real-world computational biology problems

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Product type Paperback
Published in Sep 2022
Publisher Packt
ISBN-13 9781803236421
Length 360 pages
Edition 3rd Edition
Languages
Tools
Concepts
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Author (1):
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Tiago Antao Tiago Antao
Author Profile Icon Tiago Antao
Tiago Antao
Tiago Antao is a bioinformatician currently working in the field of genomics. A former computer scientist, Tiago moved into 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 (UK). Postdoctoral, Tiago has worked with human datasets at the University of Cambridge (UK) and with mosquito whole genome sequencing data at the University of Oxford (UK), before helping to set up the bioinformatics infrastructure at the University of Montana. He currently works as a data engineer in the biotechnology field in Boston, MA. He is one of the co-authors of Biopython, a major bioinformatics package written in Python.
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Toc

Table of Contents (15) Chapters Close

Preface 1. Chapter 1: Python and the Surrounding Software Ecology 2. Chapter 2: Getting to Know NumPy, pandas, Arrow, and Matplotlib FREE CHAPTER 3. Chapter 3: Next-Generation Sequencing 4. Chapter 4: Advanced NGS Data Processing 5. Chapter 5: Working with Genomes 6. Chapter 6: Population Genetics 7. Chapter 7: Phylogenetics 8. Chapter 8: Using the Protein Data Bank 9. Chapter 9: Bioinformatics Pipelines 10. Chapter 10: Machine Learning for Bioinformatics 11. Chapter 11: Parallel Processing with Dask and Zarr 12. Chapter 12: Functional Programming for Bioinformatics 13. Index 14. Other Books You May Enjoy

Index

As this ebook edition doesn't have fixed pagination, the page numbers below are hyperlinked for reference only, based on the printed edition of this book.

Symbols

1,000 Genomes Project

URL 65

A

admixture

reference link 177

used, for investigating population structure 177-183

African Yorubans (YRI) 57

Ag3.0 data downloads

reference link 292

Amazon Web Services (AWS) 305

AmiGO

reference link 149

Anaconda

used for installing prerequisite software 2-7

annotations

used, for extracting genes from reference with 137-140

Apache Airflow

URL 249

Apache Arrow

used, for accelerating pandas processing 32-35

application programming interface (API) 50, 296

API key

used, for accessing Galaxy 252-260

Arlequin software suite

reference link 200

B

BAM format

reference link 72

Basic Local Alignment Search Tool (BLAST) 54

binary Variant Call Format (BCF)

reference link 75

BioBlend

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Authors (1)

Profile icon Tiago Antao
Tiago Antao
Github icon
Tiago Antao is a bioinformatician currently working in the field of genomics. A former computer scientist, Tiago moved into 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 (UK). Postdoctoral, Tiago has worked with human datasets at the University of Cambridge (UK) and with mosquito whole genome sequencing data at the University of Oxford (UK), before helping to set up the bioinformatics infrastructure at the University of Montana. He currently works as a data engineer in the biotechnology field in Boston, MA. He is one of the co-authors of Biopython, a major bioinformatics package written in Python.
Read more
See other products by Tiago Antao
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