DEG Part - Ref Based RNA Seq - Transcriptomics - GTN

transcriptomics-ref-based/deg-analysis

Author(s)
Bérénice Batut, Mallory Freeberg, Mo Heydarian, Anika Erxleben, Pavankumar Videm, Clemens Blank, Maria Doyle, Nicola Soranzo, Peter van Heusden, Lucille Delisle
Version
8
Last updated
Jul 5, 2024
License
MIT
Tags
transcriptomics

Features
Tutorial
Reference-based RNA-Seq data analysis
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00244
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
length
output
outfile
output
deseq_out
output
deseq_out
counts_out
out_file1
output
output
counts_out
table
out_file1
out_file1
out_file1
out_file1
out_file1
out_file1
out_file1
out_file1
wallenius_tab
wallenius_tab
wallenius_tab
wallenius_tab
out_file1
output
counts_out
out_file1
out_file1
out_file1
out_file1
out_file1
out_file1
ℹ️ Input Collection
Input Dataset Collection
ℹ️ Input Dataset
Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz
ℹ️ Input Dataset
header
ℹ️ Input Dataset
KEGG pathways to plot
Extract samples’ name
Compute gene length
Extract groups
Change Case
Tag elements with groups
Differential Analysis
Compute
Annotate DESeq2/DEXSeq output tables
Table Compute
Cut
Concatenate datasets
Table Compute
Change Case
Filter
goseq
goseq
Cut
Filter
Filter
Filter
Filter
Filter
Pathview
Join two Datasets
Group
Group
Cut
heatmap2
heatmap2
Output
DESeq2_plots
Output
DESeq2_normalized_counts
Output
DESeq2_annotated_results_with_header
Output
z_score
Output
go_genes
Output
go_plot
Output
go_terms
Output
kegg_genes
Output
kegg_pathways
Output
go_underrepresented
Output
go_overrepresented
Output
kegg_underrepresented
Output
kegg_overrepresented
Output
pathview_plot
Output
go_underrepresented_categories
Output
go_overrepresented_categories
Output
heatmap_log
Output
heatmap_zscore

Inputs

Input Label
Input dataset collection Input Dataset Collection
Input dataset Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz
Input dataset header
Input dataset KEGG pathways to plot

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0 DESeq2 Differential Analysis
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1 Concatenate datasets
toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0 Table Compute
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0 goseq
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0 goseq
Filter1 Filter
Filter1 Filter
Filter1 Filter
Filter1 Filter
toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0 Pathview
Grouping1 Group
Grouping1 Group
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3.1+galaxy0 heatmap2
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3.1+galaxy0 heatmap2

Tools

Tool Links
ChangeCase
Cut1
Filter1
Grouping1
__TAG_FROM_FILE__
join1
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/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/devteam/column_maker/Add_a_column1/2.0 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/deg_annotate/deg_annotate/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0 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
24 a1251f286 2024-07-05 09:38:54 Removed 'comments' tags
23 7d1cc771a 2024-07-05 09:15:02 Updated tools in 'DEG Part' workflow
22 41dead43e 2023-05-02 10:31:07 add mo orcid to workflows
21 36eb5cf82 2023-04-28 17:26:00 update workflows and tests
20 bba94e019 2023-04-25 09:47:41 fix workflow of DEG
19 639885e9c 2023-04-25 08:06:12 fix deseq2 params
18 0e8a4c42b 2023-04-25 07:58:48 fix input label in workflow deg
17 8fc9c9026 2023-04-25 07:46:15 add creators and licence to workflows
16 e9ac61d9e 2023-04-25 07:32:39 update deg-analysis workflow
15 543df91d6 2023-01-11 16:53:40 Update Compute tool to latest version
14 47113bebd 2022-06-30 15:22:32 Fix additional error
13 f5e192fc7 2022-06-30 14:29:26 Fix workflow
12 815b50713 2022-04-15 15:14:47 fix header parameter in deseq2 workflow
11 d377962b2 2022-04-14 22:18:06 update workflow
10 19e4e0680 2022-04-14 12:29:01 update DEG wf and test
9 d3beb91a7 2022-04-14 08:30:39 update deg-analysis workflow and test
8 a6e8658a7 2022-04-13 16:01:54 update workflow for part2
7 e08c38b2b 2022-04-05 19:36:51 add tag
6 e675ce786 2022-04-05 13:27:17 small updates
5 35d565217 2022-04-05 13:18:22 update workflows
4 05462ddf4 2022-04-05 11:54:45 update workflow
3 667ff3de9 2020-01-22 10:59:29 annotation
2 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
1 e477f2b7f 2019-09-10 09:22:59 Split workflow and add more tests

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/workflows/deg-analysis.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