PDX Volumetric Analyzer

The PDX Volumetric Analyzer is a Shiny app for uploading, validating, plotting, and analyzing your tumor volume data.

Overview

This repo offers the source code for the app's Docker image, including the Dockerfile and the app built. The app features PDX Volumetric Data uploading, validating, plotting, and analyzing your tumor volume data.

This README gives a brief introduction to pull the Docker image and run the app locally. For detailed usage of the app and more deployment options, please check our User manual under Help page.

Installation

First of all, please make sure that Docker is installed in your system, and the docker commands are available from the terminal. If not, here is the official installation guide.

Pull or build the image

To pull the pre-built Docker image from its Docker Hub repo, use:

docker pull sonerkoc/tumor-volume-suite

Alternatively, you can choose to build the image, which could take a few minutes:

git clone https://github.com/skoc/tumor-volume-shiny.git
cd tumor-volume-shiny
docker build . -t tumor-volume-shiny

Run the container

If the image was pulled from Docker Hub, use

docker run --rm -p 3838:3838 --name sb sonerkoc/tumor-volume-suite

If the image was built locally, use

docker run --rm -p 3838:3838 --name sb tumor-volume-shiny

Open the app

After the container is running, open http://127.0.0.1:3838 in your web browser.

Clean up the container and image

docker rm -f sb
docker rmi sonerkoc/tumor-volume-suite

docker rm -f sb
docker rmi tumor-volume-suite

LICENSE

This project is licensed under GNU GPLv3.

AUTHORS

Soner Koc, SevenBridges
Mike Lloyd, The Jackson Laboratory

CITATIONS

This application relies on heavily modified code originally from DRAP

Quanxue Li, Wentao Dai, Jixiang Liu, Yi‑Xue Li, and Yuan‑Yuan Li. DRAP: a toolbox for drug response analysis and visualization tailored for preclinical drug testing on patient-derived xenograft models. Journal of Translational Medicine, 2019, 17(1): 39.

The following libraries are used:

shiny
    Chang W, Cheng J, Allaire J, Sievert C, Schloerke B, Xie Y, Allen J, McPherson J, Dipert A, Borges B (2021). _shiny:
    Web Application Framework for R_. R package version 1.7.1, <URL: https://CRAN.R-project.org/package=shiny>.

plotly
    Sievert C (2020). _Interactive Web-Based Data Visualization with R, plotly, and shiny_. Chapman and Hall/CRC. ISBN
    9781138331457, <URL: https://plotly-r.com>.

dygraphs
    Vanderkam D, Allaire J, Owen J, Gromer D, Thieurmel B (2018). _dygraphs: Interface to 'Dygraphs' Interactive Time
    Series Charting Library_. R package version 1.1.1.6, <URL: https://CRAN.R-project.org/package=dygraphs>.

shinyWidgets
    Perrier V, Meyer F, Granjon D (2022). _shinyWidgets: Custom Inputs Widgets for Shiny_. R package version 0.7.1,
    <URL: https://CRAN.R-project.org/package=shinyWidgets>.

plyr
    Wickham H (2011). “The Split-Apply-Combine Strategy for Data Analysis.” _Journal of Statistical Software_, *40*(1),
    1-29. <URL: https://www.jstatsoft.org/v40/i01/>.

dplyr
    Wickham H, François R, Henry L, Müller K (2022). _dplyr: A Grammar of Data Manipulation_. R package version 1.0.8,
    <URL: https://CRAN.R-project.org/package=dplyr>.

zoo
    Zeileis A, Grothendieck G (2005). “zoo: S3 Infrastructure for Regular and Irregular Time Series.” _Journal of
    Statistical Software_, *14*(6), 1-27. doi: 10.18637/jss.v014.i06 (URL: https://doi.org/10.18637/jss.v014.i06).

ggpubr
    Kassambara A (2020). _ggpubr: 'ggplot2' Based Publication Ready Plots_. R package version 0.4.0, <URL:
    https://CRAN.R-project.org/package=ggpubr>.

grid
    R Core Team (2022). _R: A Language and Environment for Statistical Computing_. R Foundation for Statistical
    Computing, Vienna, Austria. <URL: https://www.R-project.org/>.

gridExtra
    Auguie B (2017). _gridExtra: Miscellaneous Functions for "Grid" Graphics_. R package version 2.3, <URL:
    https://CRAN.R-project.org/package=gridExtra>.

gtable
    Wickham H, Pedersen T (2019). _gtable: Arrange 'Grobs' in Tables_. R package version 0.3.0, <URL:
    https://CRAN.R-project.org/package=gtable>.

shinydashboard
    Chang W, Borges Ribeiro B (2021). _shinydashboard: Create Dashboards with 'Shiny'_. R package version 0.7.2, <URL:
    https://CRAN.R-project.org/package=shinydashboard>.

reactable
    Lin G (2022). _reactable: Interactive Data Tables Based on 'React Table'_. R package version 0.3.0, <URL:
    https://CRAN.R-project.org/package=reactable>.

bcrypt
    Ooms J (2018). _bcrypt: 'Blowfish' Password Hashing Algorithm_. R package version 1.1, <URL:
    https://CRAN.R-project.org/package=bcrypt>.

shinyBS
    Bailey E (2022). _shinyBS: Twitter Bootstrap Components for Shiny_. R package version 0.61.1, <URL:
    https://CRAN.R-project.org/package=shinyBS>.

shinyjs
    Attali D (2021). _shinyjs: Easily Improve the User Experience of Your Shiny Apps in Seconds_. R package version
    2.1.0, <URL: https://CRAN.R-project.org/package=shinyjs>.

shinyFeedback
    Merlino A, Howard P (2021). _shinyFeedback: Display User Feedback in Shiny Apps_. R package version 0.4.0, <URL:
    https://CRAN.R-project.org/package=shinyFeedback>.

shinycssloaders
    Sali A, Attali D (2020). _shinycssloaders: Add Loading Animations to a 'shiny' Output While It's Recalculating_. R
    package version 1.0.0, <URL: https://CRAN.R-project.org/package=shinycssloaders>.

shinyAce
    Nijs V, Fang F, Trestle Technology, LLC, Allen J (2022). _shinyAce: Ace Editor Bindings for Shiny_. R package
    version 0.4.2, <URL: https://CRAN.R-project.org/package=shinyAce>.

jsonlite
    Ooms J (2014). “The jsonlite Package: A Practical and Consistent Mapping Between JSON Data and R Objects.”
    _arXiv:1403.2805 [stat.CO]_. <URL: https://arxiv.org/abs/1403.2805>.

magrittr
    Bache S, Wickham H (2022). _magrittr: A Forward-Pipe Operator for R_. R package version 2.0.3, <URL:
    https://CRAN.R-project.org/package=magrittr>.

knitr
    Xie Y (2022). _knitr: A General-Purpose Package for Dynamic Report Generation in R_. R package version 1.38, <URL:
    https://yihui.org/knitr/>.
    Xie Y (2015). _Dynamic Documents with R and knitr_, 2nd edition. Chapman and Hall/CRC, Boca Raton, Florida. ISBN
    978-1498716963, <URL: https://yihui.org/knitr/>.
    Xie Y (2014). “knitr: A Comprehensive Tool for Reproducible Research in R.” In Stodden V, Leisch F, Peng RD (eds.),
    _Implementing Reproducible Computational Research_. Chapman and Hall/CRC. ISBN 978-1466561595, <URL:
    http://www.crcpress.com/product/isbn/9781466561595>.

DT
    Xie Y, Cheng J, Tan X (2022). _DT: A Wrapper of the JavaScript Library 'DataTables'_. R package version 0.22, <URL:
    https://CRAN.R-project.org/package=DT>.

readxl
    Wickham H, Bryan J (2022). _readxl: Read Excel Files_. R package version 1.4.0, <URL:
    https://CRAN.R-project.org/package=readxl>.

survival
    Therneau T (2021). _A Package for Survival Analysis in R_. R package version 3.2-13, <URL:
    https://CRAN.R-project.org/package=survival>.

Terry M. Therneau, Patricia M. Grambsch (2000). _Modeling Survival Data: Extending the Cox Model_. Springer, New
York. ISBN 0-387-98784-3.

survminer
    Kassambara A, Kosinski M, Biecek P (2021). _survminer: Drawing Survival Curves using 'ggplot2'_. R package version
    0.4.9, <URL: https://rpkgs.datanovia.com/survminer/index.html>.

validate
    van der Loo MPJ, de Jonge E (2021). “Data Validation Infrastructure for R.” _Journal of Statistical Software_,
    *97*(10), 1-31. doi: 10.18637/jss.v097.i10 (URL: https://doi.org/10.18637/jss.v097.i10).

multcomp
    Hothorn T, Bretz F, Westfall P (2008). “Simultaneous Inference in General Parametric Models.” _Biometrical Journal_,
    *50*(3), 346-363.

validate
    van der Loo MPJ, de Jonge E (2021). “Data Validation Infrastructure for R.” _Journal of Statistical Software_,
    *97*(10), 1-31. doi: 10.18637/jss.v097.i10 (URL: https://doi.org/10.18637/jss.v097.i10).

purrr
    Henry L, Wickham H (2020). _purrr: Functional Programming Tools_. R package version 0.3.4, <URL:
    https://CRAN.R-project.org/package=purrr>.

stringr
    Wickham H (2019). _stringr: Simple, Consistent Wrappers for Common String Operations_. R package version 1.4.0,
    <URL: https://CRAN.R-project.org/package=stringr>.

shinyalert
    Attali D, Edwards T (2021). _shinyalert: Easily Create Pretty Popup Messages (Modals) in 'Shiny'_. R package version
    3.0.0, <URL: https://CRAN.R-project.org/package=shinyalert>.

MikeWLloyd/tumor-volume-shiny