APL

For data exploration and finding condition-specific genes using the Association Plots.

For more details, please see our tutorial.

Introduction

APL is an interactive application developed using R package Shiny. After uploading the input matrix and choosing the parameters, the tool generates the 2D- and 3D-representation of the data, as well as the Association Plot for any selected condition or set of conditions. To identify the condition-specific genes one can zoom in the generated Association Plot and click the mouse over the genes presented in the plot. The tool allows also for enrichment analysis of the condition-specific genes for Gene Ontology terms (based on R package topGO).

Installation and usage

APL can be run directly from R, however it also requires Python. Before running the tool, please make sure that that the following R packages are installed on your machine:

• shiny
• reticulate
• ggplot2
• plotly
• dplyr
• shinycssloaders
• shinyjs
• topGO
• Rgraphviz
• org.Hs.eg.db
• org.Mm.eg.db

Also, please make sure that Python and two following Python libraries are installed on your machine:

• numpy
• torch

To use APL we recommend first to download our GitHub repository to your working directory and unzip the downloaded file. Next, to run the tool - open an R session and type following commands:

    # load shiny library
    library(shiny)
    
    # run the tool (please make sure that the folder "APL-master" is located in your working directory)
    runApp("APL-master")

Instead of downloading the entire GitHub repository you can also first create a new directory "APL-master" on your machine, and next, save there all files and folders from our GitHub repository that are required to launch APL (app.R, img_folder). Make sure that the directory "APL-master" is located in the working directory in your R session.

Alternatively, you can download and launch APL using following commands in R:

    # load shiny library
    library(shiny)
   
    # run the tool
    runGitHub("APL","elagralinska")  

To start the analysis using APL an input matrix in a tab-delimited .txt format has to be provided. The example of such file can be found here.

Demo

For demonstration purposes an example subset of GTEx data have been provided here. The provided file contains gene expression values across 22 distinct human tissues, 10 samples per each. To learn more how to analyze such data using APL see our tutorial.