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You're reading from  R Bioinformatics Cookbook - Second Edition

Product typeBook
Published inOct 2023
PublisherPackt
ISBN-139781837634279
Edition2nd Edition
Concepts
Bioinformatics
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Author (1)
Dan MacLean
Dan MacLean
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Dan MacLean

Professor Dan MacLean has a PhD in molecular biology from the University of Cambridge and gained postdoctoral experience in genomics and bioinformatics at Stanford University in California. Dan is now an honorary professor at the School of Computing Sciences at the University of East Anglia. He has worked in bioinformatics and plant pathogenomics, specializing in R and Bioconductor, and has developed analytical workflows in bioinformatics, genomics, genetics, image analysis, and proteomics at the Sainsbury Laboratory since 2006. Dan has developed and published software packages in R, Ruby, and Python, with over 100,000 downloads combined.
Read more about Dan MacLean

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Using bioconda to install external tools

Using environments for packages in R is extremely useful for managing different versions for different projects. Bioinformatics pipelines often have numerous dependencies outside of R, including binary command-line programs and packages from other languages, and it can often be useful to put those under the same sort of management. Tools for that do exist.

Anaconda is a distribution of Python and R that is particularly popular for scientific computing, data science, and machine learning. It includes a large number of pre-installed packages and tools, such as NumPy, SciPy, and Jupyter, making it easy to get started with those technologies. Anaconda also includes the conda package manager, which can be used to install additional packages and manage environments. Bioconda is a distribution of bioinformatics software built on top of conda. It includes a wide variety of bioinformatics tools and libraries, making it easy to install and manage those...

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R Bioinformatics Cookbook - Second Edition
Published in: Oct 2023Publisher: PacktISBN-13: 9781837634279
© 2023 Packt Publishing Limited All Rights Reserved

Author (1)

author image
Dan MacLean

Professor Dan MacLean has a PhD in molecular biology from the University of Cambridge and gained postdoctoral experience in genomics and bioinformatics at Stanford University in California. Dan is now an honorary professor at the School of Computing Sciences at the University of East Anglia. He has worked in bioinformatics and plant pathogenomics, specializing in R and Bioconductor, and has developed analytical workflows in bioinformatics, genomics, genetics, image analysis, and proteomics at the Sainsbury Laboratory since 2006. Dan has developed and published software packages in R, Ruby, and Python, with over 100,000 downloads combined.
Read more about Dan MacLean

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