immunarch-shiny - A Shiny application for visualizing immune repertoire statistics

Introduction

immunarch-shiny is a simple application allowing user to upload their data and immediately get plots for various immune repertoires features. Currently only diversity estimation is available.

Project Goals

• Make possible analysis of immune repertoires without R knowledge
• Speed up the process of scientific insights generation

Requirements

Imports:

    heatmap3 (>= 1.1.6),
    ggrepel (>= 0.8.0),
    reshape2 (>= 1.4.2),
    factoextra (>= 1.0.4),
    fpc,
    circlize,
    MASS (>= 7.3),
    Rtsne (>= 0.15),
    readr (>= 1.3.1),
    readxl (>= 1.3.1),
    shiny (>= 1.4.0),
    shinythemes,
    treemap,
    airr,
    ggseqlogo,
    UpSetR (>= 1.4.0),
    stringr (>= 1.4.0),
    ggalluvial (>= 0.10.0),
    Rcpp (>= 1.0),
    magrittr,
    tibble (>= 2.0),
    methods,
    scales,
    ggpubr (>= 0.2),
    rlang (>= 0.4),
    plyr,
    dbplyr (>= 1.4.0)

Depends:

    R (>= 3.5.0),
    ggplot2 (>= 3.1.0),
    dplyr (>= 0.8.0),
    dtplyr (>= 1.0.0),
    data.table (>= 1.12.6),
    gridExtra (>= 2.2.1),
    immunarch (>= 0.5.5)

Suggests:

    knitr (>= 1.8),
    roxygen2 (>= 3.0.0),
    testthat (>= 2.1.0),
    pkgdown (>= 0.1.0),
    assertthat,
    sparklyr (>= 1.0)

Instructions

Launch Shiny app from terminal:

R -e "shiny::runApp('path/to/shiny/app')"

Then go connect to app in browser navigating to address and port from terminal. Alternatively, you can open application code in R Studio and launch by Run App button.

Examples

1. Basic example, showing diversity between all samples in test dataset, estimated using Chao1.
2. Samples grouped by sex and status:

References

• R programming language (https://r-project.org/)
• Shiny framework (https://shiny.rstudio.com/)
• Mastering Shiny, tutorial under early development (https://mastering-shiny.org)
• immunarch package for immune data analysis (https://immunarch.com/)
• Miho, E., Yermanos, A., Weber, C.R., Berger, C.T., Reddy, S.T. and Greiff, V., 2018. Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires. Frontiers in immunology, 9, p.224.

Authors

Shamil Urazbakhtin - [email protected]