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Workflow Type: Galaxy

This workflow can only work on an experimental setup with exactly 2 conditions. It takes two collections of count tables as input and performs differential expression analysis. Additionally it filters for DE genes based on adjusted p-value and log2 fold changes thresholds. It also generates informative plots.

SEEK ID: https://workflowhub.eu/workflows/1201?version=1

Inputs

ID Name Description Type
Adjusted p-value threshold Adjusted p-value threshold Adjusted p-value threshold to call genes as differentially expressed. If not set, default 0.05 is used.
  • float?
Count files have header Count files have header Usually, count files generated from featureCounts tool have a header line whereas count files from RNA-STAR do not have.
  • boolean
Counts from changed condition Counts from changed condition Counts from experimental condition or changed condition. For eg. counts from treatment or knockdown samples.
  • File[]
Counts from reference condition Counts from reference condition Counts from reference condition or base condition. For eg. counts from untreated or wildtype samples.
  • File[]
Gene Annotaton Gene Annotaton The same annotation GTF used for mapping and counting
  • File
log2 fold change threshold log2 fold change threshold log2 fold change threshold to filter for highly regulated genes. If not set, default 1.0 is used.
  • float?

Steps

ID Name Description
5 Create text file toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1
7 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
8 Text transformation toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1
9 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
10 Differential Analysis toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2
11 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
12 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
13 Annotate DESeq2/DEXSeq output tables toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0
14 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
15 Annotate DESeq2 table toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1
16 Parse parameter value param_value_from_file
17 Filter with p-adj threshold Filter1
18 Generate Valcanot plot of DE genes toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6
19 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
20 Filter with log2 FC threshold Filter1
21 Join two Datasets join1
22 Cut Cut1
23 Generate Heatmap of counts toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3.1+galaxy0
24 Generate Heatmap of Z-scores 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
Annotated DESeq2 results table Annotated DESeq2 results table n/a
  • File
Volcano Plot of DE genes Volcano Plot of DE genes n/a
  • File
Significantly differentially expressed genes Significantly differentially expressed genes n/a
  • File
Heatmap of log transformed normalized counts Heatmap of log transformed normalized counts n/a
  • File
Heatmap of Z-scores Heatmap of Z-scores n/a
  • File

Version History

v0.4 (latest) Created 26th Mar 2025 at 09:50 by WorkflowHub Bot

Updated to v0.4


Frozen v0.4 bf67022

v0.3 Created 7th Feb 2025 at 03:01 by WorkflowHub Bot

Updated to v0.3


Frozen v0.3 2530a50

v0.2 Created 19th Nov 2024 at 03:02 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 2969275

v0.1 (earliest) Created 13th Nov 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 d0491c7
help Creators and Submitter
Creator
Submitter
Tools
DESeq2
ggplot2
License
MIT License (MIT)
Activity

Views: 3543   Downloads: 6217   Runs: 0

Created: 13th Nov 2024 at 03:02

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