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:- run velocity calculations (run
run_3.Compute-RNA-velocity.sh
) - plot them (run
run_4.Velocity.estimate-to-Velocity_plot.sh
orrun_make_separate_arrow_plots.sh
).
- run velocity calculations (run
-
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.