10  Installation

Follow the steps below to install the latest development version of MAPA Shiny App from GitHub (the script first installs BiocManager, remotes, and MAPA if you don’t have them):

if (!requireNamespace("BiocManager", quietly = TRUE)) {
 install.packages("BiocManager") 
}

if (!requireNamespace("remotes", quietly = TRUE)) {
 install.packages("remotes") 
}

remotes::install_github(
  "jaspershen-lab/mapa",
  dependencies = TRUE,
  repos = BiocManager::repositories(),
  upgrade = "ask"
)

remotes::install_github(
  "jaspershen-lab/mapashiny",
  dependencies = TRUE,
  repos        = BiocManager::repositories(),
  upgrade      = "ask"
)
Note

Possible Dependency Conflict: If mapa installation failed because the simplifyEnrichment version is incompatible, update Bioconductor to version 3.20 or newer. To do that, you’ll need R environment 4.4.0 or newer.

Tip

What is MAPA Shiny App: The Shiny-app version for MAPA lets you run the complete MAPA workflow with points and clicks without any R coding skills. It’s especially handy for bench scientists and those who prefer a graphical UI.

How to Launch the Shiny App:

  1. In an R session, run:mapashiny::run_mapa_shiny()

  2. An R viewer window will open where you can start the workflow. You can also use the Open in Browser button (top-right) to launch the app in your default web browser.

  3. You can stop the app at any time by closing the browser tab/window or pressing the stop button in your R IDE.

10.1 Web-based Access to MAPA

A hosted, browser-based instance of MAPA is available for users who prefer not to manage a local R environment. The service provides the same point-and-click interface as the Shiny application and requires no installation.

Access URL: https://mapashiny.jaspershenlab.com

Note

The workflow described in this section is applicable to both MAPA Shiny App and the web-based MAPA platform.

10.1.1 Getting Started

  1. Open the URL above in a modern web browser
  2. Follow this tutorial to upload input data and configure analysis parameters
  3. Launch the workflow and monitor progress in the browser
  4. Download figures, tables, and reports upon completion
Important

Data Privacy Statement

  • Yes, your uploaded data are transmitted to and processed by our server.

  • No, we do not sell your data, use your data to train machine-learning models, or make your files public.

Uploaded files are used solely to run the analysis you request and are kept in session-scoped, temporary storage that is routinely purged.

If your dataset is confidential, regulated, or requires strict control over storage location and retention, prefer the local Shiny deployment under your organization’s governance.

Note

We’re excited that the MAPA web and MAPA Shinyapp are already available and working well. However, some webpage features and graphical layouts are still under active development. This means the version you see might look slightly different from the examples present in this tutorial.

These updates are part of our ongoing effort to improve your experience and make things better step by step. Thank you sincerely for your patience and understanding.