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

Example run command:

nextflow run main.nf 
	--mae_object path/to/h5MAE/ 
	--output output/dir 
	--r_config bin/Analysis/config.yml 
	--isa_file path/to/20240822_Xomics_iPSC_Neurons_new_READ-ONLY.xlsx 
	--markers_dir path/to/Markers_files/
	--alt_omics_dir path/to/iPSC_MAE/

Example run command in Digital Research Environment (DRE):

• Need to specify dre.config and container_dir wit .sif files

nextflow run main.nf 
	--mae_object /mnt/data/data/iPSC_data/iPSC_MAE/h5MAE/ 
	-c dre.config 
	--container_dir /mnt/data/software/singularity/ 
	--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 
	--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/

Licenses

=======

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

Example run command:

nextflow run main.nf 
	--mae_object path/to/h5MAE/ 
	--output output/dir 
	--r_config bin/Analysis/config.yml 
	--isa_file path/to/20240822_Xomics_iPSC_Neurons_new_READ-ONLY.xlsx 
	--markers_dir path/to/Markers_files/
	--alt_omics_dir path/to/iPSC_MAE/

Example run command in Digital Research Environment (DRE):

• Need to specify dre.config and container_dir wit .sif files

nextflow run main.nf 
	--mae_object /mnt/data/data/iPSC_data/iPSC_MAE/h5MAE/ 
	-c dre.config 
	--container_dir /mnt/data/software/singularity/ 
	--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 
	--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/