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.
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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 |
|
| 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) |
|
| 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) |
|
| 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: 1099 Downloads: 113
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, 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, 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, WES, 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, Euro-BioImaging, EOSC-Life WP3 OC Team, cross RI project, ANSES-Ploufragan, SANBI Pathogen Bioinformatics, Biodata Analysis Group, DeSci Labs, Erasmus MC - Viroscience Bioinformatics, ARA-dev, Mendel Centre for Plant Genomics and Proteomics, Metagenomic tools, WorkflowEng, Polygenic Score Catalog, bpm, scNTImpute, Systems Biotechnology laboratory, Cimorgh IT solutions, MLme: Machine Learning Made Easy, Hurwitz Lab, Dioscuri TDA, Scipion CNB, System Biotechnology laboratory, yPublish - Bioinfo tools, NIH CFDE Playbook Workflow Partnership, MMV-Lab, EMBL-CBA, EBP-Nor, Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data, Bioinformatics Laboratory for Genomics and Biodiversity (LBGB), multi-analysis dFC, CholGen, RNA group, Plant Genomes Pipelines in Galaxy, Pathogen Genomic Laboratory, Chemical Data Lab, JiangLab, Pangenome database project, HP2NET - Framework for construction of phylogenetic networks on High Performance Computing (HPC) environment, Center for Open Bioimage Analysis, Generalized Open-Source Workflows for Atomistic Molecular Dynamics Simulations of Viral Helicases, Historical DNA genome skimming, QCDIS, Peter Menzel's Team, NHM Clark group, ESRF Workflow System (Ewoks), Kalbe Bioinformatics, Nextflow4Metabolomics, GBCS, CEMCOF
Web page: Not specified
Space: Independent Teams
Public web page: https://ipc-project.eu/
Start date: 1st Jan 2019
End date: 31st May 2023
