iPSC Data Analysis

Description

This project is part of the Dutch X-omics initiative and focuses on the analysis of multi-omics data from several iPSC lines. The data included genomics, transcriptomics, proteomics, and several different types of metabolomics.

Goal

The goal is to identify disease-specific traits of the patient-derived iPSC compared to various control lines.

Pipeline overview

File outline

|- README.md     # This readme\ |- Data analysis plan.md ...

EATRIS-Plus Multi-omics Analysis Workflow

Analysis workflow used to analyze the cohort of healthy blood donors

Prerequisites

Multi-omics data set from Zenodo

• The data is stored in a Multi_Assay_Experiment object, which is used as input for the workflow
• The object can be downloaded here: https://doi.org/10.5281/zenodo.10782799

Install Nextflow using conda

Create a Conda Environment:

conda create -n nextflow-env 
conda activate nextflow-env 
conda install -c bioconda
...

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 ...