In jdgagnon/DE.AHC: DE.AHC

knitr::opts_chunk$set(
  collapse = TRUE,
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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 If you do not already have R installed, or your version is out of date, download and install the latest version.

2. Optionally, install the latest version of RStudio Desktop.

3. Download the package from GitHub

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

2. Load your own differential expression data file

3. File should be structured like:

knitr::kable(
  matrix(c("Cd28", 2.4, 0.0000342, 0.0004244, 50, 48, 49, 62, 58, 60,
           rep("etc...", 10)), 
         ncol = 10, byrow = T), 
  col.names = c("Gene", "logFC", "PValue", "FDR", "WT_1", "WT_2", "WT_3", "cKO_1", "cKO_2", "cKO_3"))

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

knitr::kable(
  matrix(c("Cd28", "3UTR", "mmu-miR-16-5p", TRUE, 2899,
           rep("etc...", 5)), 
         ncol = 5, byrow = T), 
  col.names = c("Gene", "Location", "miR", "Targetscan", "Sum"))

Session info

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

sessionInfo()

License

GNU GPL-3.0-or-later

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