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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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Estimating differential expression with edgeR

The edgeR package in Bioconductor is a tool for identifying differentially expressed genes from RNA-Seq data. It offers a range of normalization methods for correcting differences in library size and sequencing depth, including the trimmed mean of M-values (TMM) method. TMM is a popular normalization method that uses the mean of log-transformed expression values to scale the data, taking into account the differences in library size between samples.

In addition to normalization, edgeR also provides a range of statistical models for testing differential expression. One of the main models used in edgeR is the negative binomial model, which is a type of generalized linear model (GLM) that is well-suited for modeling count data such as RNA-Seq data. The negative binomial model allows for the estimation of the mean and dispersion of the expression counts, and can account for overdispersion, which is common in RNA-Seq data. Overall, edgeR is...

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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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