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 # Description of the data analysis plan (DAP)
|- DAP.png        # Overview image of step 4 and 5 of the DAP

Software and packages used

• R version 4.3.2 in the software folder (Z:\software\R)

Data sources

• CNV WES (Z:\data\iPSC_data\iPSC_CNV-WES\README.md)
• RNA-seq (Z:\data\iPSC_data\iPSC_RNAseq\README.md)
• Proteomics (Z:\data\iPSC_data\iPSC_proteomics\README.md)
• Metabolomics (RUMC, Nijmegen) (Z:\data\iPSC_data\iPSC_metabolomics_TML\README.md)
• Metabolomics and Lipidomics (LUMC, Leiden) (Z:\data\iPSC_data\iPSC_metabolomics_lipidomics_LUMC\README.md)

Digital Reserarch Environment:

Support MyDRE:

• https://support.mydre.org/

Gitlab-DRE connection errors

If Gitlab gives a timeout warning when used from within the DRE:

1. Confirm if https://gitlab.cmbi.umcn.nl/x-omics_ipscs/ipsc-data-analysis.git/ can be accessed through the browser

2. Correct the proxy configuration with the following git command:

   git config --global http.proxy http://proxy.mydre.org:3128

CRAN/Bioconductor

• Configuration instructions https://support.mydre.org/portal/en/kb/articles/proxy-configurations-rstudio#Introduction

Use a Biconductor mirror:

• Add options(BioC_mirror = "https://ftp.gwdg.de/pub/misc/bioconductor/") to the C:\Program Files\R\R-[your R version]\etc\Rprofile.site(requires DRE admin rights)

Nextflow Workflow

Run the analysis workflow using Nextflow.

Usage

nextflow run main.nf \
    -profile singularity \        # Use `-profile docker` for Docker
    --mae_object <path/to/h5MAE/> \
    --output <output/dir> \
    --r_config <bin/Analysis/config.yml> \
    --isa_file <path/to/ISA_file>

Optional parameters:

Parameter	Description
--markers_dir	Path to markers files directory
--alt_omics_dir	Path to alternative omics directory

---

Running in a Digital Research Environment (DRE)

Use the dre profile and provide a --container_dir pointing to your Singularity (.sif) files.

nextflow run main.nf \
    -profile dre \
    --container_dir /mnt/data/software/singularity/ \
    --mae_object /mnt/data/data/iPSC_data/iPSC_MAE/h5MAE/ \
    --output /output/dir \
    --r_config bin/Analysis/config.yml \
    --isa_file /mnt/data/data/iPSC_data/iPSC_MAE/20240822_Xomics_iPSC_Neurons_new_READ-ONLY.xlsx

Optional parameters:

Parameter	Description
--markers_dir	/mnt/data/data/iPSC_data/Markers_files/
--meth_dir	/mnt/data/data/iPSC_data/Meth_NF_files/
--alt_omics_dir	/mnt/data/data/iPSC_data/iPSC_MAE/

Data files on Zenodo

To run the Nextflow pipeline, input files can be downloaded on Zenodo: Link_to_Zenodo

Licenses