Differential gene expression for single-cell data using pseudo-bulk counts with edgeR

single-cell-pseudobulk-analysis/pseudo-bulk-edger

Author(s)
Diana Chiang Jurado, Pavankumar Videm, Pablo Moreno
Version
1
Last updated
Feb 12, 2025
License
CC-BY-4.0
Tags
single-cell
pseudobulk

Features
Tutorial
Pseudobulk Analysis with Decoupler and EdgeR
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00313
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
output
output
output
output
output
output
count_matrix
samples_metadata
genes_metadata
outfile
outfile
output_tabular
outfile
output
outfile
outfile
outTables
output
outTables
output
outfile
list_output_txt
output_tabular
text_param
ℹ️ Input Dataset
Source AnnData file
ℹ️ Input Parameter
Pseudo-bulk: Fields to merge
ℹ️ Input Parameter
Group by column
ℹ️ Input Parameter
Sample key column
ℹ️ Input Parameter
Name Your Raw Counts Layer
ℹ️ Input Parameter
Factor fields
ℹ️ Input Parameter
Formula
ℹ️ Input Parameter
Gene symbol column
Decoupler pseudo-bulk
Sanitize matrix
Sanitize factors
Remove start, end, width
Sanitize first factor for leading digits
Text reformatting
edgeR
Get contrast labels
Select gene symbols, logFC, PValue and FDR
Replace Text
Split contrasts
Contrast as parameters
Volcano Plot
Output
Pseudobulk count matrix
Output
Pseudobulk Plot
Output
Filtered by expression
Output
Tables: DEG
Output
Report Results: HTML File
Output
Tables for volcano plot
Output
Volcano Plot on input dataset(s): PDF

Inputs

Input Label
Input dataset Source AnnData file
Input parameter Pseudo-bulk: Fields to merge
Input parameter Group by column
Input parameter Sample key column
Input parameter Name Your Raw Counts Layer
Input parameter Factor fields
Input parameter Formula
Input parameter Gene symbol column

Outputs

From Output Label
Input parameter Pseudo-bulk: Fields to merge
Input parameter Group by column
Input parameter Sample key column
Input parameter Name Your Raw Counts Layer
Input parameter Factor fields
Input parameter Formula
Input parameter Gene symbol column
toolshed.g2.bx.psu.edu/repos/ebi-gxa/decoupler_pseudobulk/decoupler_pseudobulk/1.4.0+galaxy8 Decoupler pseudo-bulk
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5 edgeR
toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0 Remove columns Select gene symbols, logFC, PValue and FDR
toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6 Volcano Plot

Tools

Tool Links
param_value_from_file
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/decoupler_pseudobulk/decoupler_pseudobulk/1.4.0+galaxy8 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6 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
3 cc7888368 2024-12-11 14:41:36 Update pseudo-bulk_edgeR.ga
2 95f00fe4e 2024-12-11 14:33:57 Update pseudo-bulk_edgeR.ga
1 45bf38997 2024-12-06 18:55:00 Add pseudobulk-analysis tutorial and associated files

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/pseudobulk-analysis/workflows/pseudo-bulk_edgeR.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