weersmalabibd/psc_project

PSC_project

The repository for the code used in the PSC project and manuscript called "Single-cell RNA sequencing in inflammatory bowel disease in patients with primary sclerosing cholangitis: a distinct form of colitis".

The steps for replicating the results of this study are grouped into categories, and each in its own sub-directory including a README file.

Overview

For each different step of the scRNAseq analysis, separate codes were generated. Languages and packages are listed below:

• R >= 3.6.1
• Seurat >= 3.1

External tools used were:

• Souporcell v.1: https://github.com/wheaton5/souporcell
• Cellranger v.3.0.2: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation
• fido v.1.0.2: https://jsilve24.github.io/fido/articles/introduction-to-fido.html
• Cellchat v.1.4.0: http://www.cellchat.org/

Workflow

the content for each step includes these steps in this order:

• Alignment of the sequence data to the GRCh38 reference Human Genome:
• Lane integration:
• Demultiplexing, doublet_detection, and quality control (QC):
• General quality control and filtering:
• Normalization and data integration:
• Dimensional reduction and clustering:
• Cell type classification:
• Cell abundances analysis:
• Differential gene expression analysis and pathway analysis:
• Cell-cell interaction analysis:

Hardware

Analyses were performed on the Gearshift cluster http://docs.gcc.rug.nl/gearshift/cluster/