MASLD-NASH

scripts associated with MASLD-NASH project, now published in Nature

Acquisition of epithelial plasticity in human chronic liver disease, Gribben et al, 2024 https://www.nature.com/articles/s41586-024-07465-2

• alignment - use CellRanger to align fastq files

• pre-processing - read count matrices into Seurat, and preprocess gene expression data. Add cell type annotations, and apply Harmony integration. Expected run order is:

  • 1.indv-samples.Rmd
  • do_preprocessing.sh
  • generate_cellType_annotation_jan2022.R
  • apply_harmony_correction.R

  the other files are called / required by these ones.

• RNA_velocity - calculate RNA velocity using velocyto and plot it. Two steps:

  1. run velocity calculations (run run_3.Compute-RNA-velocity.sh)
  2. plot them (run run_4.Velocity.estimate-to-Velocity_plot.sh or run_make_separate_arrow_plots.sh).

• cell-cell_interaction - use CellPhoneDB to identify potentially interacting ligand-receptor pairs in different cell types. Expected run order is:

  • 1.prepare_labelled_seu_objs.R
  • 2.run_run_cellPhoneDb_clusters.sh
  • 3.Process-cellPhoneDb-output.R other scripts are required / called by these.

• Pseudotime - infer pseudotime in cholangiocyte and hepatocyte cells using Monocle3. Identify and plot genes differentially expressed over pseudotime.

• figure_scripts - scripts and helper functions to produce the near final figures.