IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0349941.html

RAGER: A user-friendly computational platform for integrated analysis of RNA-Seq and ATAC-seq data

Author

Listed:
  • Yunjie Liu
  • Yijia Liu
  • Zhouming Zhang
  • Fei Li
  • Hua Yu
  • Lu Lu

Abstract

Technical advances in RNA sequencing (RNA-seq) and Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) provide us a genome-wide method to deeper insights into gene expression and regulation. The lack of user-friendly bioinformatics platforms poses a challenge for accurately interpreting such datasets. Here, we present a computational platform, RAGER, that integrates the popular bioinformatics tools in an automated thread for joint mining of RNA-seq and ATAC-seq data. RAGER facilitates integrative analysis of transcriptome and chromatin accessibility by providing an automated workflow that minimizes the need for bioinformatics expertise and significantly reduces processing time. We demonstrate RAGER’s utility for novel biological discovery by characterizing the transcriptome and chromatin accessibility of two recently published datasets. RAGER was implemented using Snakemake and is freely available via https://github.com/bioinfo202408/RAGER.

Suggested Citation

  • Yunjie Liu & Yijia Liu & Zhouming Zhang & Fei Li & Hua Yu & Lu Lu, 2026. "RAGER: A user-friendly computational platform for integrated analysis of RNA-Seq and ATAC-seq data," PLOS ONE, Public Library of Science, vol. 21(5), pages 1-18, May.
    • Handle: RePEc:plo:pone00:0349941
    DOI: 10.1371/journal.pone.0349941
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0349941
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0349941&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0349941?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
    ---><---

    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:pone00:0349941. 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.