Phantasus, a web-application for visual and interactive gene expression analysis

  1. Maksim Kleverov
  2. Daria Zenkova
  3. Vladislav Kamenev
  4. Margarita Sablina
  5. Maxim N Artyomov
  6. Alexey A Sergushichev  Is a corresponding author
  1. ITMO University, Russian Federation
  2. Washington University in St. Louis, United States

Abstract

Transcriptomic profiling became a standard approach to quantify a cell state, which led to accumulation of huge amount of public gene expression datasets. However, both reuse of these datasets or analysis of newly generated ones requires significant technical expertise. Here we present Phantasus - a user-friendly web-application for interactive gene expression analysis which provides a streamlined access to more than 96000 public gene expression datasets, as well as allows analysis of user-uploaded datasets. Phantasus integrates an intuitive and highly interactive JavaScript-based heatmap interface with an ability to run sophisticated R-based analysis methods. Overall Phantasus allows users to go all the way from loading, normalizing and filtering data to doing differential gene expression and downstream analysis. Phantasus can be accessed on-line at https://alserglab.wustl.edu/phantasus or can be installed locally from Bioconductor (https://bioconductor.org/packages/phantasus). Phantasus source code is available at https://github.com/ctlab/phantasus under MIT license.

Data availability

The current manuscript is a computational study, so no data have been generated for this manuscript. The application source code is available at https://github.com/ctlab/phantasus under MIT licence.

The following previously published data sets were used

Article and author information

Author details

  1. Maksim Kleverov

    Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russian Federation
    Competing interests
    The authors declare that no competing interests exist.
  2. Daria Zenkova

    Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russian Federation
    Competing interests
    The authors declare that no competing interests exist.
  3. Vladislav Kamenev

    Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russian Federation
    Competing interests
    The authors declare that no competing interests exist.
  4. Margarita Sablina

    Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russian Federation
    Competing interests
    The authors declare that no competing interests exist.
  5. Maxim N Artyomov

    Department of Pathology and Immunology, Washington University in St. Louis, St Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Alexey A Sergushichev

    Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russian Federation
    For correspondence
    alsergbox@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1159-7220

Funding

Ministry of Science and Higher Education of the Russian Federation (Priority 2030 Federal Academic Leadership Program)

  • Maksim Kleverov
  • Alexey A Sergushichev

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Marisa Nicolás, Laboratório Nacional de Computação Científica, Brazil

Version history

  1. Received: December 21, 2022
  2. Accepted: May 13, 2024
  3. Accepted Manuscript published: May 14, 2024 (version 1)

Copyright

© 2024, Kleverov et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Maksim Kleverov
  2. Daria Zenkova
  3. Vladislav Kamenev
  4. Margarita Sablina
  5. Maxim N Artyomov
  6. Alexey A Sergushichev
(2024)
Phantasus, a web-application for visual and interactive gene expression analysis
eLife 13:e85722.
https://doi.org/10.7554/eLife.85722

Share this article

https://doi.org/10.7554/eLife.85722

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