Workflow Type: Common Workflow Language
Open
Stable
MultiAffinity enables the study of how gene dysregulation propagates on a multilayer network on a disease of interest, uncovering key genes. Find the detailed documentation for the tool here.
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Inputs
ID | Name | Description | Type |
---|---|---|---|
counts | n/a | Count Matrices of the RNA-Seq studies - List of input CSV files, separated by commas |
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metadata | n/a | Metadata of the RNA-Seq studies - List of input CSV files, separated by commas |
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layers | n/a | Layers of the multilayer networks - List of input CSV files, separated by commas |
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approach | n/a | Computes correlation on each community or respect all genes, local or global approach (default is local) |
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output_dir | n/a | Defines name for output folder |
|
padj | n/a | Sets significance value for DESeq2, RRA, and Spearman's Corr (default is 0.05) |
|
LFC | n/a | Defines whether self loops are removed or not, takes values 0 or 1 (default is 1) |
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control_id | n/a | Defines metadata label for the control samples (default is Normal) |
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multiXrank_r | n/a | Global restart probability for multiXrank, given by float between 0 and 1 (default is 0.15) |
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multiXrank_selfloops | n/a | Defines whether self loops are removed or not, takes values 0 or 1 (default is 1) |
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Molti_modularity | n/a | Sets Newman modularity resolution parameter on molTI-DREAM (default is 1) |
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Molti_Louvain | n/a | Switches to randomized Louvain on molTI-DREAM and sets num. of randomizations (default is 5) |
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min_nodes | n/a | Defines minimum number of nodes required to describe a community (default is 7) |
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Steps
ID | Name | Description |
---|---|---|
tool | n/a | n/a |
Outputs
ID | Name | Description | Type |
---|---|---|---|
output | n/a | Contains degs, communities and affinity information |
|
Version History
Version 1 (earliest) Created 29th Nov 2021 at 12:59 by Laura Rodriguez-Navas
Added multiaffinity-workflow.cwl
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Views: 1319 Downloads: 312
Created: 29th Nov 2021 at 12:59
Last updated: 18th Mar 2022 at 12:18
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