Proteomics: MaxQuant and MSstats LFQ workflow 3.0
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Run on GalaxyMaxQuant and MSstats for the analysis of label-free data
Associated Tutorial
This workflows is part of the tutorial Proteomics: MaxQuant and MSstats LFQ workflow, available in the GTN
Thanks to...
Tutorial Author(s): Melanie Föll, Matthias Fahrner
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| annotation file | #main/annotation file | n/a |
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| comparison matrix | #main/comparison matrix | n/a |
|
| fasta protein database | #main/fasta protein database | n/a |
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| raw files | #main/raw files | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | MaxQuant | toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy4 |
| 5 | Select | Grep1 |
| 6 | Select | Grep1 |
| 7 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 |
| 8 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 |
| 9 | MSstats | toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.22.0.1 |
| 10 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops/1.0.6 |
| 11 | Summary Statistics | Summary_Statistics1 |
| 12 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 |
| 13 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 |
| 14 | Filter | Filter1 |
| 15 | Filter | Filter1 |
| 16 | Filter | Filter1 |
| 17 | Filter | Filter1 |
| 18 | Filter | Filter1 |
| 19 | Cut | Cut1 |
| 20 | Cut | Cut1 |
| 21 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 |
| 22 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 |
| 23 | heatmap2 | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1 |
| 24 | UniProt | toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2 |
| 25 | heatmap2 | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1 |
| 26 | UniProt | toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2 |
| 27 | FASTA-to-Tabular | toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 |
| 28 | FASTA-to-Tabular | toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
| _anonymous_output_10 | #main/_anonymous_output_10 | n/a |
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| _anonymous_output_11 | #main/_anonymous_output_11 | n/a |
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| _anonymous_output_12 | #main/_anonymous_output_12 | n/a |
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| _anonymous_output_13 | #main/_anonymous_output_13 | n/a |
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| _anonymous_output_14 | #main/_anonymous_output_14 | n/a |
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| _anonymous_output_15 | #main/_anonymous_output_15 | n/a |
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| _anonymous_output_16 | #main/_anonymous_output_16 | n/a |
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| _anonymous_output_17 | #main/_anonymous_output_17 | n/a |
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| _anonymous_output_18 | #main/_anonymous_output_18 | n/a |
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| _anonymous_output_19 | #main/_anonymous_output_19 | n/a |
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| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
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| _anonymous_output_20 | #main/_anonymous_output_20 | n/a |
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| _anonymous_output_21 | #main/_anonymous_output_21 | n/a |
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| _anonymous_output_22 | #main/_anonymous_output_22 | n/a |
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| _anonymous_output_23 | #main/_anonymous_output_23 | n/a |
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| _anonymous_output_24 | #main/_anonymous_output_24 | n/a |
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| _anonymous_output_25 | #main/_anonymous_output_25 | n/a |
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| _anonymous_output_26 | #main/_anonymous_output_26 | n/a |
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| _anonymous_output_27 | #main/_anonymous_output_27 | n/a |
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| _anonymous_output_28 | #main/_anonymous_output_28 | n/a |
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| _anonymous_output_29 | #main/_anonymous_output_29 | n/a |
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| _anonymous_output_3 | #main/_anonymous_output_3 | n/a |
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| _anonymous_output_30 | #main/_anonymous_output_30 | n/a |
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| _anonymous_output_31 | #main/_anonymous_output_31 | n/a |
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| _anonymous_output_32 | #main/_anonymous_output_32 | n/a |
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| _anonymous_output_33 | #main/_anonymous_output_33 | n/a |
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| _anonymous_output_34 | #main/_anonymous_output_34 | n/a |
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| _anonymous_output_4 | #main/_anonymous_output_4 | n/a |
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| _anonymous_output_5 | #main/_anonymous_output_5 | n/a |
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| _anonymous_output_6 | #main/_anonymous_output_6 | n/a |
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| _anonymous_output_7 | #main/_anonymous_output_7 | n/a |
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| _anonymous_output_8 | #main/_anonymous_output_8 | n/a |
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| _anonymous_output_9 | #main/_anonymous_output_9 | n/a |
|
Version History
3.0 (earliest) Created 25th Jun 2024 at 11:14 by Helena Rasche
Added/updated 4 files
Open
masterf09523a
Creators and Submitter
Views: 1063 Downloads: 274 Runs: 0
Created: 25th Jun 2024 at 11:14
Last updated: 25th Jun 2024 at 11:14
Tags AttributionsNone
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