README.md

In jdgagnon/DE.AHC: DE.AHC

DE.AHC

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 miR-15/16 differential expression data along with AGO2 HITS-CLIP data for each gene.

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 If you do not already have R installed, or your version is out of date, download and install the latest version.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(“remotes”)
remotes::install_github("jgagnon/DE.AHC”)

Usage

1. Load the package into the R session.

library(DE.AHC)

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

runDEAHCapp()

1. Optionally subset genes based on pathways or list specific genes. Toggle checkbox to filter genes that contain miR-15/16 seed-matches in their 3’UTR

• Load your own differential expression data file
• File should be structured like:

| Gene | logFC | PValue | FDR | WT_1 | WT_2 | WT_3 | cKO_1 | cKO_2 | cKO_3 | | :--- | :---- | :------- | :-------- | :---- | :---- | :---- | :----- | :----- | :----- | | Cd28 | 2.4 | 3.42e-05 | 0.0004244 | 50 | 48 | 49 | 62 | 58 | 60 | | etc… | etc… | etc… | etc… | etc… | etc… | etc… | etc… | etc… | etc… |

• Load your own AGO2 HITS-CLIP data file
• File should be structured like:

| Gene | Location | miR | Targetscan | Sum | | :--- | :------- | :------------ | :--------- | :--- | | Cd28 | 3UTR | mmu-miR-16-5p | TRUE | 2899 | | etc… | etc… | etc… | etc… | etc… |

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  highr_0.7       knitr_1.20     
#> [13] stringr_1.3.1   digest_0.6.17   evaluate_0.11

License

GNU GPL-3.0-or-later

jdgagnon/DE.AHC documentation built on May 9, 2021, 2:29 a.m.