RNA Seq Genes To Pathways (imported from uploaded file)
5.0

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Workflow Type: Galaxy

RNA-seq genes to pathways

Associated Tutorial

This workflows is part of the tutorial RNA Seq Genes To Pathways (imported from uploaded file), available in the GTN

Thanks to...

Tutorial Author(s): Maria Doyle, Belinda Phipson

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1316?version=1

Inputs

ID Name Description Type
DE table #main/DE table n/a
  • array containing
    • File
factordata #main/factordata n/a
  • File
limma_filtered_counts #main/limma_filtered_counts n/a
  • File
mouse_hallmark_sets #main/mouse_hallmark_sets n/a
  • File
seqdata #main/seqdata n/a
  • File

Steps

ID Name Description
5 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6
6 Cut Cut1
7 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0
8 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0
9 Join two Datasets join1
10 Sort toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1
11 EGSEA toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0
12 Cut Cut1
13 Cut Cut1
14 fgsea toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1
15 goseq toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.44.0+galaxy0

Outputs

ID Name Description Type
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_10 #main/_anonymous_output_10 n/a
  • File
_anonymous_output_11 #main/_anonymous_output_11 n/a
  • File
_anonymous_output_12 #main/_anonymous_output_12 n/a
  • File
_anonymous_output_13 #main/_anonymous_output_13 n/a
  • File
_anonymous_output_14 #main/_anonymous_output_14 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
_anonymous_output_3 #main/_anonymous_output_3 n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File
_anonymous_output_5 #main/_anonymous_output_5 n/a
  • File
_anonymous_output_6 #main/_anonymous_output_6 n/a
  • File
_anonymous_output_7 #main/_anonymous_output_7 n/a
  • File
_anonymous_output_8 #main/_anonymous_output_8 n/a
  • File
_anonymous_output_9 #main/_anonymous_output_9 n/a
  • File

Version History

5.0 (earliest) Created 25th Jun 2024 at 11:23 by Helena Rasche

Added/updated 4 files


Open master 8b1a987
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
EGSEA
fgsea
GOseq
License
Creative Commons Attribution 4.0 International
Activity

Views: 346   Downloads: 76

Created: 25th Jun 2024 at 11:23

Last updated: 25th Jun 2024 at 11:23

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Total size: 83.5 KB
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