SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data
Publication Date
June 09, 2016
Journal
PLOS ONE
Authors
Hugo Varet, Loraine Brillet Guéguen, Jean Yves Coppée & Marie Agnès Dillies
Volume
11
Issue
6
Pages
e0157022
DOI
https://dx.plos.org/10.1371/journal.pone.0157022
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0157022
Web of Science
000377563000069
Scopus
84976324043
Mendeley
http://www.mendeley.com/research/sartools-deseq2-edgerbased-r-pipeline-comprehensive-differential-analysis-rnaseq-data
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Mendeley | Further Information

{"title"=>"SARTools: A DESeq2- and edgeR-based R pipeline for comprehensive differential analysis of RNA-Seq data", "type"=>"journal", "authors"=>[{"first_name"=>"Hugo", "last_name"=>"Varet", "scopus_author_id"=>"55352160300"}, {"first_name"=>"Loraine", "last_name"=>"Brillet-Guéguen", "scopus_author_id"=>"56888723200"}, {"first_name"=>"Jean Yves", "last_name"=>"Coppée", "scopus_author_id"=>"55916699000"}, {"first_name"=>"Marie Agnès", "last_name"=>"Dillies", "scopus_author_id"=>"12771098900"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"610893112", "sgr"=>"84976324043", "issn"=>"19326203", "pmid"=>"27280887", "scopus"=>"2-s2.0-84976324043", "doi"=>"10.1371/journal.pone.0157022", "isbn"=>"1932-6203 (Electronic) 1932-6203 (Linking)"}, "id"=>"57d7e7de-fe9a-3624-a0e5-48afde6a726e", "abstract"=>"Background Several R packages exist for the detection of differentially expressed genes from RNA-Seq data. The analysis process includes three main steps, namely normalization, dispersion estimation and test for differential expression. Quality control steps along this process are recommended but not mandatory, and failing to check the characteristics of the dataset may lead to spurious results. In addition, normalization methods and statistical models are not exchangeable across the packages without adequate transformations the users are often not aware of. Thus, dedicated analysis pipelines are needed to include systematic quality control steps and prevent errors from misusing the proposed methods. Results SARTools is an R pipeline for differential analysis of RNA-Seq count data. It can handle designs involving two or more conditions of a single biological factor with or without a blocking factor (such as a batch effect or a sample pairing). It is based on DESeq2 and edgeR and is composed of an R package and two R script templates (for DESeq2 and edgeR respectively). Tuning a small number of parameters and executing one of the R scripts, users have access to the full results of the analysis, including lists of differentially expressed genes and a HTML report that (i) displays diagnostic plots for quality control and model hypotheses checking and (ii) keeps track of the whole analysis process, parameter values and versions of the R packages used. Conclusions SARTools provides systematic quality controls of the dataset as well as diagnostic plots that help to tune the model parameters. It gives access to the main parameters of DESeq2 and edgeR and prevents untrained users from misusing some functionalities of both packages. By keeping track of all the parameters of the analysis process it fits the requirements of reproducible research.", "link"=>"http://www.mendeley.com/research/sartools-deseq2-edgerbased-r-pipeline-comprehensive-differential-analysis-rnaseq-data", "reader_count"=>186, "reader_count_by_academic_status"=>{"Unspecified"=>9, "Professor > Associate Professor"=>5, "Researcher"=>55, "Student > Doctoral Student"=>12, "Student > Ph. D. Student"=>52, "Student > Postgraduate"=>7, "Student > Master"=>25, "Other"=>7, "Student > Bachelor"=>8, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>9, "Professor > Associate Professor"=>5, "Researcher"=>55, "Student > Doctoral Student"=>12, "Student > Ph. D. Student"=>52, "Student > Postgraduate"=>7, "Student > Master"=>25, "Other"=>7, "Student > Bachelor"=>8, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>14, "Agricultural and Biological Sciences"=>90, "Veterinary Science and Veterinary Medicine"=>3, "Chemistry"=>1, "Computer Science"=>11, "Engineering"=>2, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>47, "Mathematics"=>3, "Medicine and Dentistry"=>5, "Neuroscience"=>2, "Pharmacology, Toxicology and Pharmaceutical Science"=>2, "Immunology and Microbiology"=>4}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>5}, "Mathematics"=>{"Mathematics"=>3}, "Unspecified"=>{"Unspecified"=>14}, "Environmental Science"=>{"Environmental Science"=>2}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>2}, "Engineering"=>{"Engineering"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Neuroscience"=>{"Neuroscience"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>90}, "Computer Science"=>{"Computer Science"=>11}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>47}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>3}}, "reader_count_by_country"=>{"New Zealand"=>1, "Netherlands"=>1, "United States"=>4, "Japan"=>1, "Brazil"=>1, "United Kingdom"=>1, "Israel"=>1, "Germany"=>1, "Spain"=>1}, "group_count"=>6}

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Scopus | Further Information

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