BactEXTRACT: an R Shiny app to quickly extract, plot and analyse bacterial growth and gene expression data

  1. Julien Dénéréaz
  2. Jan-Willem Veening

Reviewed by

Read the full article See related articles

Discuss this preprint

Start a discussion What are Sciety discussions?

Listed in

This article is not in any list yet, why not save it to one of your lists.
Log in to save this article

Abstract

To streamline the analysis and visualization of bacterial growth and gene expression data obtained by microtitre plate readers, we developed BactEXTRACT, an intuitive, easy-to-use R Shiny application. BactEXTRACT simplifies the transition from raw optical density, fluorescence and luminescence measurements to publication-ready plots. This package offers a user-friendly interface that reduces the complexity involved in growth curve and gene expression analysis and is generally applicable. BactEXTRACT is available at https://veeninglab.com/bactextract .

Article activity feed

  2. Version published to 10.1099/acmi.0.000742.v3 on Access Microbiology
  3. Version published to 10.1099/acmi.0.000742.v2 on Access Microbiology
  4. Access Microbiology

    The work presented is clear and the arguments well formed. This study would be a valuable contribution to the existing literature. This is a study that would be of interest to the field and community. Thank you for your submission, reviewers raised only minor amendments, once delt with, we will be happy to accept. The manuscript was well written and the tool will be valuable. I would like to raise an issue with the webtool on low resolution or small screens (or when the window is tiled on screen). While resolvable by zooming, initially there are some lay out issues. No requirements to resolve but raised incase this is an easy fix for you.

  5. Access Microbiology

    Comments to Author

    Line 26 - 'very deeply' should be changed to 'deeply' Line 34 - 'amounts' should be changed to 'amount' Line 36 - Refers to figure 1A, a microplate reader. However, the context is that it is referencing microplate software. Either the figure or reference should be as not to make it appear the authors are referencing software while showing a figure of the hardware. Line 41- 'Strain' and 'Treatment' shouldn't be capitalised Otherwise a sound paper and a nice to use package

    Please rate the manuscript for methodological rigour

    Good

    Please rate the quality of the presentation and structure of the manuscript

    Good

    To what extent are the conclusions supported by the data?

    Strongly support

    Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?

    No

    Is there a potential financial or other conflict of interest between yourself and the author(s)?

    No

    If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?

    No: No human/animal work

  6. Access Microbiology

    Comments to Author

    The manuscript of Dénéréaz & Veening describes the development and implementation of an incredibly useful R based software tool called BactEXTRACT, which is implemented as a Shiny to allow real time web-based plotting of data. The application also has a very helpful storage facility to enable reproducible plotting of data. The provision of example data is also useful to users to enable data to be formatted correctly, should they not be using certain brands of plate reader. There is also the likelihood that that this app could be used for the analysis of data from Cell Growth Quantifier systems at scale too. The software uses the Growthcurver R app to analyse the data, which provides robust analysis framework and through BactEXTRACT is easier to implement without the requirement for R skills from the user. All data is available, the software works and the Github links function. Overall the software will be very useful to the community and will find wide potential applications across microbiology. The manuscript is well written and I have no changes for the authors to make and I look forward to seeing it published.

    Please rate the manuscript for methodological rigour

    Very good

    Please rate the quality of the presentation and structure of the manuscript

    Very good

    To what extent are the conclusions supported by the data?

    Strongly support

    Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?

    No

    Is there a potential financial or other conflict of interest between yourself and the author(s)?

    No

    If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?

    Yes

  7. Version published to 10.1099/acmi.0.000742.v1 on Access Microbiology