multiaffinity-workflow
Version 1

Workflow Type: Common Workflow Language
Stable

drawing

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.

alt

Inputs

ID Name Description Type
counts n/a Count Matrices of the RNA-Seq studies - List of input CSV files, separated by commas
  • File[]
metadata n/a Metadata of the RNA-Seq studies - List of input CSV files, separated by commas
  • File[]
layers n/a Layers of the multilayer networks - List of input CSV files, separated by commas
  • File[]?
approach n/a Computes correlation on each community or respect all genes, local or global approach (default is local)
  • string?
output_dir n/a Defines name for output folder
  • string?
padj n/a Sets significance value for DESeq2, RRA, and Spearman's Corr (default is 0.05)
  • string?
LFC n/a Defines whether self loops are removed or not, takes values 0 or 1 (default is 1)
  • string?
control_id n/a Defines metadata label for the control samples (default is Normal)
  • string?
multiXrank_r n/a Global restart probability for multiXrank, given by float between 0 and 1 (default is 0.15)
  • string?
multiXrank_selfloops n/a Defines whether self loops are removed or not, takes values 0 or 1 (default is 1)
  • int?
Molti_modularity n/a Sets Newman modularity resolution parameter on molTI-DREAM (default is 1)
  • int?
Molti_Louvain n/a Switches to randomized Louvain on molTI-DREAM and sets num. of randomizations (default is 5)
  • int?
min_nodes n/a Defines minimum number of nodes required to describe a community (default is 7)
  • int?

Steps

ID Name Description
tool n/a n/a

Outputs

ID Name Description Type
output n/a Contains degs, communities and affinity information
  • Directory

Version History

Version 1 (earliest) Created 14th Dec 2021 at 10:01 by Laura Rodriguez-Navas

Updated multiaffinity-workflow.cwl


Open master 581e04b
help Creators and Submitter
Creator
Additional credit

Mar Batlle

Submitter
Activity

Views: 234   Downloads: 7

Created: 14th Dec 2021 at 10:01

Last updated: 18th Mar 2022 at 12:22

Last used: 28th Jun 2022 at 16:00

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Total size: 2.5 KB
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