Visualization Of RNA-Seq Results With Volcano Plot

transcriptomics-rna-seq-viz-with-volcanoplot/visualization-of-rna-seq-results-with-volcano-plot

Author(s)
Maria Doyle, Armin Dadras, Helena Rasche
Version
1
Last updated
Apr 17, 2025
License
CC-BY-4.0
Tags
transcriptomics
visualization

Features
Tutorial
Visualization of RNA-Seq results with Volcano Plot
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:
RO-Crate logo with flask Download Workflow RO-Crate
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nDE results"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nVolcano genes"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Volcano plot highlighting significant"];
  0 -->|output| 2;
  3["Volcano plot labelling top 10"];
  0 -->|output| 3;
  4["Volcano plot labelling genes of interest"];
  0 -->|output| 4;
  1 -->|output| 4;
  16aef53e-11fd-4def-a7fb-6cf9a98f0902["Output\nvolcano_pdf"];
  4 --> 16aef53e-11fd-4def-a7fb-6cf9a98f0902;
  style 16aef53e-11fd-4def-a7fb-6cf9a98f0902 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset DE results
Input dataset Volcano genes

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.7 Volcano Plot Volcano plot labelling genes of interest

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.7 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands On: Importing a workflow
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
1 cbbd91ced 2025-04-11 15:06:27 Updated the tutorial, workflow and tools of rna-seq-viz-with-volcanoplot for GTA2025

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/workflows/Visualization-Of-RNA-Seq-Results-With-Volcano-Plot.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows