README.md

In jdgagnon/microRNA.TEvMP: Display graph of microRNA expression among TE and MP populations

microRNA.TEvMP

by John D. Gagnon University of California, San Francisco

Table of Contents

Overview Installation Usage Session info License

Overview

A shinyapp-based GUI to visualize microRNA expression over time in response to infection with LCMV. Uses data from Khan, A.A., L.A. Penny, Y. Yuzefpolskiy, S. Sarkar, and V. Kalia. 2013. MicroRNA-17∼92 regulates effector and memory CD8 T-cell fates by modulating proliferation in response to infections. Blood. 121:4473–4483. .

Installation

1. If you do not already have R installed, or your version is out of date, download and install the latest version.

• Optionally, install the latest version of RStudio Desktop.

1. Download the package from GitHub

install.packages("devtools")
devtools::install_github("jdgagnon/microRNA.TEvMP")

Usage

1. Load the package into the R session.

library(microRNA.TEvMP)

1. To initialize the shiny app, paste the following code in your R console and run it.

microRNA.TEvMP()

1. Select one or more microRNAs from the dropdown menu to be highlighted.

Session info

Here is the output of sessionInfo() on the system on which this package was developed:

sessionInfo()
#> R version 3.5.1 (2018-07-02)
#> Platform: x86_64-apple-darwin17.6.0 (64-bit)
#> Running under: macOS High Sierra 10.13.6
#> 
#> Matrix products: default
#> BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
#> LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] compiler_3.5.1  backports_1.1.2 magrittr_1.5    rprojroot_1.3-2
#>  [5] tools_3.5.1     htmltools_0.3.6 yaml_2.2.0      Rcpp_0.12.18   
#>  [9] stringi_1.2.4   rmarkdown_1.10  knitr_1.20      stringr_1.3.1  
#> [13] digest_0.6.17   evaluate_0.11

License

GNU GPL-3.0-or-later

jdgagnon/microRNA.TEvMP documentation built on May 9, 2019, 5:06 a.m.