IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0157022.html
   My bibliography  Save this article

SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data

Author

Listed:
  • Hugo Varet
  • Loraine Brillet-Guéguen
  • Jean-Yves Coppée
  • Marie-Agnès Dillies

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.

Suggested Citation

  • Hugo Varet & Loraine Brillet-Guéguen & Jean-Yves Coppée & Marie-Agnès Dillies, 2016. "SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data," PLOS ONE, Public Library of Science, vol. 11(6), pages 1-8, June.
  • Handle: RePEc:plo:pone00:0157022
    DOI: 10.1371/journal.pone.0157022
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0157022
    Download Restriction: no

    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0157022&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pone.0157022?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Maxime Mistretta & Mena Cimino & Pascal Campagne & Stevenn Volant & Etienne Kornobis & Olivier Hebert & Christophe Rochais & Patrick Dallemagne & Cédric Lecoutey & Camille Tisnerat & Alban Lepailleur , 2024. "Dynamic microfluidic single-cell screening identifies pheno-tuning compounds to potentiate tuberculosis therapy," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
    2. Erminia Donnarumma & Michael Kohlhaas & Elodie Vimont & Etienne Kornobis & Thibault Chaze & Quentin Giai Gianetto & Mariette Matondo & Maryse Moya-Nilges & Christoph Maack & Timothy Wai, 2022. "Mitochondrial Fission Process 1 controls inner membrane integrity and protects against heart failure," Nature Communications, Nature, vol. 13(1), pages 1-24, December.
    3. Chrats Melkonian & Francisco Zorrilla & Inge Kjærbølling & Sonja Blasche & Daniel Machado & Mette Junge & Kim Ib Sørensen & Lene Tranberg Andersen & Kiran R. Patil & Ahmad A. Zeidan, 2023. "Microbial interactions shape cheese flavour formation," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    4. Chih-Yao Chung & Kritarth Singh & Vassilios N. Kotiadis & Gabriel E. Valdebenito & Jee Hwan Ahn & Emilie Topley & Joycelyn Tan & William D. Andrews & Benoit Bilanges & Robert D. S. Pitceathly & Gyorgy, 2021. "Constitutive activation of the PI3K-Akt-mTORC1 pathway sustains the m.3243 A > G mtDNA mutation," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    5. Sarah L. Sokol-Borrelli & Sarah M. Reilly & Michael J. Holmes & Stephanie B. Orchanian & Mackenzie D. Massmann & Katherine G. Sharp & Leah F. Cabo & Hisham S. Alrubaye & Bruno Martorelli Di Genova & M, 2023. "A transcriptional network required for bradyzoite development in Toxoplasma gondii is dispensable for recrudescent disease," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    6. Kirill Grigorev & Theodore M. Nelson & Eliah G. Overbey & Nadia Houerbi & JangKeun Kim & Deena Najjar & Namita Damle & Evan E. Afshin & Krista A. Ryon & Jean Thierry-Mieg & Danielle Thierry-Mieg & Ari, 2024. "Direct RNA sequencing of astronaut blood reveals spaceflight-associated m6A increases and hematopoietic transcriptional responses," Nature Communications, Nature, vol. 15(1), pages 1-11, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0157022. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.