Visualization Of RNA-Seq Results With Volcano Plot

transcriptomics-rna-seq-viz-with-volcanoplot/rna-seq-viz-with-volcanoplot

Author(s)

Version
6
Last updated
Jun 21, 2021
License
None Specified, defaults to CC-BY-4.0
Tags
transcriptomics

Features
Tutorial
Visualization of RNA-Seq results with Volcano Plot
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00253
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
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/0.0.5 Volcano Plot Volcano plot labelling genes of interest

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5 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
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on Import at the top-right of the screen
  • 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”
  • 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
8 470fa5796 2021-06-18 20:12:15 Fix name
7 086ac3f50 2021-06-18 20:09:12 Update workflow
6 2e2cb42d8 2020-10-04 11:59:11 add tests from workflow-testing for blockclust and rna-seq-viz-with-volcano-plot, edit workflows
5 667ff3de9 2020-01-22 10:59:29 annotation
4 f7f017f33 2020-01-15 12:40:00 dna and rna capitals
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 faf6d298a 2019-12-12 13:02:33 unflatten workflows
1 47566efc6 2019-07-05 14:38:11 Add workflow to volcanoplot tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/workflows/rna-seq-viz-with-volcanoplot.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