multiAffinity Version 1
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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.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| counts | n/a | Count Matrices of the RNA-Seq studies - List of input CSV files, separated by commas |
|
| metadata | n/a | Metadata of the RNA-Seq studies - List of input CSV files, separated by commas |
|
| layers | n/a | Layers of the multilayer networks - List of input CSV files, separated by commas |
|
| approach | n/a | Computes correlation on each community or respect all genes, local or global approach (default is local) |
|
| 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) |
|
| 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) |
|
| multiXrank_selfloops | n/a | Defines whether self loops are removed or not, takes values 0 or 1 (default is 1) |
|
| 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) |
|
| min_nodes | n/a | Defines minimum number of nodes required to describe a community (default is 7) |
|
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 14th Dec 2021 at 10:01 by Laura Rodriguez-Navas
Frozen
Version-1581e04b
Creators and Submitter
Views: 657 Downloads: 12
Created: 14th Dec 2021 at 10:01
Last updated: 21st Apr 2023 at 12:06
AttributionsNone
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Teams: GalaxyProject SARS-CoV-2, nf-core viralrecon, EOSC-Life - Demonstrator 7: Rare Diseases, iPC: individualizedPaediatricCure, EJPRD WP13 case-studies workflows, TransBioNet, OpenEBench, ELIXIR Proteomics
Organizations: Barcelona Supercomputing Center (BSC-CNS), ELIXIR
https://orcid.org/0000-0003-4929-1219
Computer Engineer in Barcelona Supercomputing Center (BSC)
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Teams: IBISBA Workflows, NMR Workflow, UNLOCK, NanoGalaxy, Galaxy Climate, PNDB, IMBforge, COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource, LBI-RUD, Nick-test-team, usegalaxy-eu, Italy-Covid-data-Portal, UX trial team, Integrated and Urban Plant Pathology Laboratory, SARS-CoV-2 Data Hubs, lmjxteam2, virAnnot pipeline, Ay Lab, iPC: individualizedPaediatricCure, Harkany Lab, Genomics Coordination Center, EJPRD WP13 case-studies workflows, Common Workflow Language (CWL) community, Testing, SeBiMER, IAA-CSIC, MAB - ATGC, Probabilistic graphical models, GenX, Snakemake-Workflows, ODA, IPK BIT, CO2MICS Lab, FAME, CHU Limoges - UF9481 Bioinformatique / CNR Herpesvirus, Quadram Institute Bioscience - Bioinformatics, HecatombDevelopment, Institute of Human Genetics, Testing RO Crates, Test Team, Applied Computational Biology at IEG/HMGU, INFRAFRONTIER workflows, OME, TransBioNet, OpenEBench, Galaxycompchem, Bioinformatics and Biostatistics (BIO2 ) Core, VIB Bioinformatics Core, CRC Cohort, ICAN, MustafaVoh, Single Cell Unit, CO-Graph, emo-bon, TestEMBL-EBIOntology, CINECA, Toxicology community, Pitagora-Network, Workflows Australia, Medizinisches Proteom-Center, Medical Bioinformatics, AGRF BIO, EU-Openscreen, X-omics, ELIXIR Belgium, URGI, Size Inc, GA-VirReport Team, The Boucher Lab, Cluster Emergent del Cervell Humà, Air Quality Prediction, pyiron, CAPSID, Edinburgh Genomics, Defragmentation TS, NBIS, Phytoplankton Analysis, Seq4AMR, Workflow registry test, Read2Map, SKM3, ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression, de.NBI Cloud, Meta-NanoSim, ILVO Plant Health, EMERGEN-BIOINFO, KircherLab, Apis-wings, BCCM_ULC, Dessimoz Lab, TRON gGmbH, GEMS at MLZ, Computational Science at HZDR, Big data in biomedicine, TRE-FX, MISTIC, Guigó lab, Statistical genetics, Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation, DLSW, Bioinformatics Unit @ CRG, Bioinformatics Innovation Lab, BSC-CES, ELIXIR Proteomics, Black Ochre Data Labs, Zavolan Lab, Metabolomics-Reproducibility, Team Cardio, NGFF Tools, Bioinformatics workflows for life science, Workflows for geographic science, Pacific-deep-sea-sponges-microbiome, CSFG, SNAKE, Katdetectr, INFRAFRONTIER GmbH, PerMedCoE, EuroScienceGateway
Web page: Not specified
Space: Independent Teams
Public web page: https://ipc-project.eu/
Start date: 1st Jan 2019
End date: 31st May 2023
