Workflow Type: Nextflow

This workflow is designed to analyze to a multi-omics data set that comprises genome-wide DNA methylation profiles, targeted metabolomics, and behavioral data of two cohorts that participated in the ACTION Biomarker Study (ACTION, Aggression in Children: Unraveling gene-environment interplay to inform Treatment and InterventiON strategies. (Boomsma 2015, Bartels 2018, Hagenbeek 2020, van Dongen 2021, Hagenbeek 2022). The ACTION-NTR cohort consists of twins that are either longitudinally concordant or discordant for childhood aggression. The ACTION-Curium-LUMC cohort consists of children referred to the Dutch LUMC Curium academic center for child and youth psychiatry. With the joint analysis of multi-omics data and behavioral data, we aim to identify substructures in the ACTION-NTR cohort and link them to aggressive behavior. First, the individuals are clustered using Similarity Network Fusion (SNF, Wang 2014), and latent feature dimensions are uncovered using different unsupervised methods including Multi-Omics Factor Analysis (MOFA) (Argelaguet 2018) and Multiple Correspondence Analysis (MCA, Lê 2008, Husson 2017). In a second step, we determine correlations between -omics and phenotype dimensions, and use them to explain the subgroups of individuals from the ACTION-NTR cohort. In order to validate the results, we project data of the ACTION-Curium-LUMC cohort onto the latent dimensions and determine if correlations between omics and phenotype data can be reproduced.

Version History

Version 2.3 (latest) Created 24th Nov 2023 at 13:50 by Casper de Visser

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Frozen Version-2.3 3ec2ed7

Version 2.2 Created 15th May 2023 at 13:27 by Casper de Visser

Update RO-Crate, Docker containers are added as SoftwareRequirements. DOI to Zenodo pages are linked. DOI to Zenodo page of the ISA files is added as well.

Frozen Version-2.2 c16057e

Version 2.0 Created 3rd Feb 2023 at 14:31 by Casper de Visser

Frozen Version-2.0 c15dde8

Version 4 Created 7th Dec 2022 at 15:01 by Casper de Visser

Synced with Github commit d90fb662f3dc8a77fafe0c1a8688a78c50d5bf2b;

Frozen Version-4 0c2508d

Version 1.2 Created 8th Nov 2022 at 15:46 by Casper de Visser

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Frozen Version-1.2 d86abc2

Version 1.1 Created 26th Oct 2022 at 11:00 by Casper de Visser

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Frozen Version-1.1 f5a1374

Version 1 (earliest) Created 26th Oct 2022 at 09:19 by Casper de Visser

RO-Crate made from Github page, at commit be1cfd2c8680d32e8bd741b116fafbeb74323b9c

Frozen Version-1 848ac01
help Creators and Submitter
De Visser, C., & Niehues, A. (2023). X-omics ACTIONdemonstrator analysis workflow. WorkflowHub.

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Created: 26th Oct 2022 at 09:19

Last updated: 8th Aug 2023 at 10:06

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