We are analyzing https://link.springer.com/protocol/10.1007/978-1-4939-3578-9_19.

Title:
It’s DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR | SpringerLink
Description:
RNA sequencing (RNA-seq) is widely used to profile transcriptional activity in biological systems. Here we present an analysis pipeline for differential expression analysis of RNA-seq experiments using the Rsubread and edgeR software packages. The basic pipeline...
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Keywords {🔍}

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Topics {✒️}

high-throughput sequencing data month download article/chapter multifactor rna-seq experiments org/smyth/pubs/robustebayespreprint rna sequencing data privacy choices/manage cookies mccarthy dj differential expression analysis moderated statistical tests eliza hall institute medical research council rna-sequence data gene expression estimation device instant download rna-seq data differential expression analyses author information authors rna-seq experiments including complex comparisons gene set testing detecting differential expression european economic area profile transcriptional activity mammary gland cells quantifying mammalian transcriptomes scalable read mapping shrunken dispersion estimates small-sample estimation negative binomial dispersion egf-mediated induction alveolar cell survival discovering splice junctions vernon puzey scholarship assessing differential expression journal finder publish conditions privacy policy quasi-likelihood features complex microarray experiments statistical genomics accepting optional cookies quasi-likelihood methods scaling normalization method main content log edger software packages check access empirical bayes methods ethics access dna sequencing yunshun chen & gordon national institutes

Schema {🗺️}

ScholarlyArticle:
      headline:It’s DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR
      pageEnd:416
      pageStart:391
      image:https://media.springernature.com/w153/springer-static/cover/book/978-1-4939-3578-9.jpg
      genre:
         Springer Protocols
      isPartOf:
         name:Statistical Genomics
         isbn:
            978-1-4939-3578-9
            978-1-4939-3576-5
         type:Book
      publisher:
         name:Springer New York
         logo:
            url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
            type:ImageObject
         type:Organization
      author:
            name:Aaron T. L. Lun
            affiliation:
                  name:Walter and Eliza Hall Institute of Medical Research
                  address:
                     name:Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Yunshun Chen
            affiliation:
                  name:Walter and Eliza Hall Institute of Medical Research
                  address:
                     name:Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Gordon K. Smyth
            affiliation:
                  name:Walter and Eliza Hall Institute of Medical Research
                  address:
                     name:Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
                     type:PostalAddress
                  type:Organization
            type:Person
      keywords:RNA-seq, Differential expression, Generalized linear models, Quasi-likelihood, Variability, Read alignment, Read counts
      description:RNA sequencing (RNA-seq) is widely used to profile transcriptional activity in biological systems. Here we present an analysis pipeline for differential expression analysis of RNA-seq experiments using the Rsubread and edgeR software packages. The basic pipeline includes read alignment and counting, filtering and normalization, modelling of biological variability and hypothesis testing. For hypothesis testing, we describe particularly the quasi-likelihood features of edgeR. Some more advanced downstream analysis steps are also covered, including complex comparisons, gene ontology enrichment analyses and gene set testing. The code required to run each step is described, along with an outline of the underlying theory. The chapter includes a case study in which the pipeline is used to study the expression profiles of mammary gland cells in virgin, pregnant and lactating mice.
      datePublished:2016
      isAccessibleForFree:
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Book:
      name:Statistical Genomics
      isbn:
         978-1-4939-3578-9
         978-1-4939-3576-5
Organization:
      name:Springer New York
      logo:
         url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
         type:ImageObject
      name:Walter and Eliza Hall Institute of Medical Research
      address:
         name:Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
         type:PostalAddress
      name:Walter and Eliza Hall Institute of Medical Research
      address:
         name:Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
         type:PostalAddress
      name:Walter and Eliza Hall Institute of Medical Research
      address:
         name:Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
         type:PostalAddress
ImageObject:
      url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
Person:
      name:Aaron T. L. Lun
      affiliation:
            name:Walter and Eliza Hall Institute of Medical Research
            address:
               name:Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
               type:PostalAddress
            type:Organization
      name:Yunshun Chen
      affiliation:
            name:Walter and Eliza Hall Institute of Medical Research
            address:
               name:Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
               type:PostalAddress
            type:Organization
      name:Gordon K. Smyth
      affiliation:
            name:Walter and Eliza Hall Institute of Medical Research
            address:
               name:Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
               type:PostalAddress
            type:Organization
PostalAddress:
      name:Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
      name:Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
      name:Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
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