DEG Part - Ref Based RNA Seq - Transcriptomics - GTN

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Workflow Type: Galaxy

Reference-based RNA-Seq data analysis

Associated Tutorial

This workflows is part of the tutorial DEG Part - Ref Based RNA Seq - Transcriptomics - GTN, available in the GTN

Features

Thanks to...

Tutorial Author(s): Bérénice Batut, Mallory Freeberg, Mo Heydarian, Anika Erxleben, Pavankumar Videm, Clemens Blank, Maria Doyle, Nicola Soranzo, Peter van Heusden, Lucille Delisle

Tutorial Contributor(s): Helena Rasche, Clea Siguret

Workflow Author(s): Bérénice Batut, Mallory Freeberg, Mo Heydarian, Anika Erxleben, Pavankumar Videm, Clemens Blank, Maria Doyle, Nicola Soranzo, Peter van Heusden, Lucille Delisle

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1326?version=3

Inputs

ID Name Description Type
Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz gene annotation
  • File
Input Dataset Collection Input Dataset Collection Counts obtained by Feature counts
  • File[]
KEGG pathways to plot KEGG pathways to plot selected KEGG pathways to plot
  • File
header header header for annotated DESeq2 output
  • File

Steps

ID Name Description
4 Extract samples' name toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
5 Compute gene length toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2
6 Extract groups toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1
7 Change Case ChangeCase
8 Tag elements with groups __TAG_FROM_FILE__
9 Differential Analysis toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0
10 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
11 Annotate DESeq2/DEXSeq output tables toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0
12 Table Compute toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0
13 Cut Cut1
14 Concatenate datasets toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1
15 Table Compute toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0
16 Change Case ChangeCase
17 Filter Filter1
18 goseq toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0
19 goseq toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0
20 Cut Cut1
21 Filter Filter1
22 Filter Filter1
23 Filter Filter1
24 Filter Filter1
25 Filter Filter1
26 Pathview toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0
27 Join two Datasets join1
28 Group Grouping1
29 Group Grouping1
30 Cut Cut1
31 heatmap2 toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3.1+galaxy0
32 heatmap2 toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3.1+galaxy0

Outputs

ID Name Description Type
DESeq2_plots DESeq2_plots n/a
  • File
DESeq2_normalized_counts DESeq2_normalized_counts n/a
  • File
DESeq2_annotated_results_with_header DESeq2_annotated_results_with_header n/a
  • File
z_score z_score n/a
  • File
go_genes go_genes n/a
  • File
go_plot go_plot n/a
  • File
go_terms go_terms n/a
  • File
kegg_genes kegg_genes n/a
  • File
kegg_pathways kegg_pathways n/a
  • File
go_underrepresented go_underrepresented n/a
  • File
go_overrepresented go_overrepresented n/a
  • File
kegg_underrepresented kegg_underrepresented n/a
  • File
kegg_overrepresented kegg_overrepresented n/a
  • File
pathview_plot pathview_plot n/a
  • File
go_underrepresented_categories go_underrepresented_categories n/a
  • File
go_overrepresented_categories go_overrepresented_categories n/a
  • File
heatmap_log heatmap_log n/a
  • File
heatmap_zscore heatmap_zscore n/a
  • File

Version History

8.0 (latest) Created 16th Jul 2024 at 14:05 by Helena Rasche

Added/updated 4 files


Open master 13c5f15

24.0 Created 5th Jul 2024 at 14:24 by Helena Rasche

Added/updated 4 files


Frozen 24.0 b90c65e

22.0 (earliest) Created 25th Jun 2024 at 11:25 by Helena Rasche

Added/updated 4 files


Frozen 22.0 c080d1f
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
R
DESeq2
GOseq
pathview
ggplot2
License
MIT License (MIT)
Activity

Views: 2006   Downloads: 758   Runs: 0

Created: 25th Jun 2024 at 11:24

Last updated: 5th Jul 2024 at 14:24

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Total size: 303 KB
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